This is an awesome mod, nicely done and going nicer with time considering the amount and quality of the numerous updates. I've some experience in modding ww2 armies (albeit at a lesser scale) so I know it's a huge, painful job you've done.
I've not read every single post of the thread so sorry if there are some redundancies in these comments.
I-Tanks
Here are some glitches I noticed:
Preliminary remark: British tanks need some love, there are lots that could get upgrades from 2pdr to 6pdr guns etc. the way the German Panzers get upgrades. Besides a lot of them were used by the Red army too - and to a lesser extent by the Free French but probably not beyond company level so not in the current scope?
1) The British early tanks (cruiser and infantry alike until 1942 and the 6 pounder guns of the crusader III/valentine VIII) had no heavy explosive (HE) ammunitions at all, so they are currently overpowered against infantry! The infantry was supposed to do job, not the tanks. They were also vulnerable to AT guns because of their shorter range (both types) and thin armour (in the case of cruisers), to the point that it was a common German tactic to draw British cruisers towards hidden AT guns in the desert... There were some close support variants of the cruisers and Matilda II, but they probably wouldnt make much of a difference with at division level (they were for HQ units iirc).
This probably means you do indeed need a specific class for the Matilda II (as mentioned somewhere), and one for British cruisers (except the crusader Mk III) or you'd end with BT-2/BT-7 having a penalty against infantry they might not deserve... besides the difference in armour thickness isn't deserving the British cruiser MkIII compared to the BT7 (30mn max v 22mn for the later BT7s). It might be of lesser import compared to the lack of HE ammunition but it's worth keeping in mind too. I suggest having them in the different classes anyway.
2) The Valentine was not a light tank, the armour thickness was only slightly less than the Matilda (but 10mm thicker than say the PkwIII), it had the same gun however so it shouldn't get a penalty against armour. Same class as Matilda but a little faster or new class too? I suppose the Valentine VIII and its QF6 gun could go to the same tank class as the Pz III except they were way slower (24 km/h v 40km/h). New class or that can be done with the various sql files?
3) The Hotchkiss 35 tanks had some antitank issues (and the R35 since it had the same gun). Conversely the Tetrach (same class) had the same gun as most British tanks of the time (the QF2 that also equipped the Cruisers until the QF6 replaced it) but very thin armour (14mm max compared to the H35 max 34-40mm) so they also shouldn't be in the same class (early tank destroyer?). As the L6/40 had similar armour to the H35 and a 20mm gun I guess you can keep these two in the same class... but the Panzer 35(t) had thinner armour (25mm) and a better gun... than the French/Italian ones so shouldn't be in the same class either (but probably in the same as the Tetrach).
4) Only the earlier T-26 had only machine guns, so you should add an upgraded T-26 model 1933 with the 45mm AT gun and put it in the same class as Pz II/H39... but the M3 had significantly more armour than both (51mm), and the H39 (34mm) significantly more than the Pz II (14mm) so the M3 (and later the M5 Stuart) might deserve a separate class (again!)
5) Should there really be light tanks divisions after 1940? Except maybe the Red Army early nobody really used them as divisions (or rather brigades I think), maybe they should be there only for scenarios (like Stalingrad) or as companies (battalion, regiment?) for recce/éclairage/aufklärung no idea of the Russian term sorry - (even more so after 1943 when western allies scrapped light tank regiments)?
6) Though certainly not light or cavalry, the Pz IV was not designed to fight tanks, but to support other tanks against infantry. In the mod it's currently the king of the hill in 1940 which certainly wasn't true! Its main gun was no match for the frontal armour of the Matilda 2, B1bis or even the Somua, and both British 2pdr and French 47 mm could penetrate its armour (well provided the Luftwaffe wasn't around of course). Maybe the Pz IV E or F deserves being introduced after the fall of France, with its upgraded armour and for the F, upgraded gun?
7) Speaking of German tanks, the German armoured forces of 1940 were mostly (2/3) made of Pz I and II (and to a lesser extend of Skoda 35(t) rather than Pz III/IV, so it would be nice to prevent the German AI building of so many III and IV... from what I've seen so far it's more like a 50/50 ratio and almost no infantry (which is really not realistic see below). The German Heer had concentrated its armour far more than the French, which certainly deserves a bonus in game terms, but right now there are too many III/IV and
8) There were 10 Panzerdivisionen in the Battle of France and 4 Divisions Cuirassées, 3 Divisions Légère Mécaniques and 1 British Armoured Division, compared to 137 divisions in the Heer, and 149 divisions in the allied forces in may 1940. The current overwhelming importance and numbers of armoured divisions is a little reminiscent of 60 years old clichés

Though ww2 saw the emergence of motorised warfare even the German armoured forces werent fully motorised until 1941 (and not any more in 1944/5), there were still many hooves and feet, and many more than wheels and tracks for most of the war and fronts! More infantry (and more infantry love)!
II- Infantry (shorter!)
1) Infantry need some love, you can't compare a 1940 French or British infantry with a 1944 one, the AT capabilities were really boosted by the bazookas or PIAT, and air supremacy made AA capacity really secondary for instance. I think (I don't have most of my sources at hand though) that they were better armed too, with more machineguns and light machine guns and AT/AA capabilities at company level (and all the more so at division level). Same for the German infantry after 1942 with the panzerfaust, I don't know for the Russian apart from the not so unsuccessful of Molotov cocktails both by the Red Army and the Finnish infantry.
Conversely in 1940, a good chunk of the French infantry was made of reserve units with old equipment and lesser AT capabilities than other units, and Infanterie de forteresse units probably didnt have any since the AT capability was fixed.
2) A much bigger proportion of the 1944 western troops were motorised which wasn't the case of the 1940 infantry (even the German one, far from it) so movement might be worth having a look into. I know you have mechanised infantry in mind, but motorised is also a big change in ww2.
3) The paratroopers and their 42 combat value are really too tough compared to the basic infantry 36.
IV- Convoys (shorter!)
1) Convoy bug: after (literally) hours of testing and some amateurish coding (I insist on that though I'll gladly send you what I've done) I'm quite sure this had to do with map complexity on the north america/europe and probably world 1936 maps (though I haven't tested it as extensively and I want to check the infamous Bombay convoy). I created some waypoints (one in the sea near Gibraltar, one NE of Miami, one near Iceland) and I've not seen a single crash since. I suspect you might want to look more closely into moveunit/isatdestination/moveconvoy too.
2) I've seen crashes with embarked troops when they return to their initial position and then try to go back to their disembark point (if the UK player manages to stem the German horde from Seelöwe for instance).
On the 1942 Europe map it seems the submarine search script might be a crash cause too (never seen it after a crash in the Lus log on the Europe or NA/Europe map).
3) I've not noticed the AI building much subs to hunt convoys, or subs hunting convoys much, in any scenario? Bug or work in progress?
V- Gameplay - ground warfare
1) Though it makes sense that very high silhouette tanks like the M3 have no defensive bonus at all (they couldn't fight hull-down after all), is the same true of the more compact tanks? or even lower silhouette Stugs and such?
2) Tanks are too powerful (at least the 1940 ones), the German success wasn't that much the Blitzkrieg (which is for the most part a mix of myth and after action propaganda there's a lot of recent research and books on that, including German ones, and testimonies from the last living actors like August von Kageneck's Lieutenant de Panzer (no English translation that I know of sadly) and Blizkrieg-Legende from Karl-Heinz Frieser are two examples) as the first use of combined arms (and lessons learned from Spain and Poland), and namely a very good use of air and artillery as a way to soften the way for the tanks (or infantry at Sedan and other places). It worked quite well for the German as long as they had air and artillery supremacy, then the tide turned... On paper the Luftwaffe didn't have such an advantage but I've read somewhere that about a third of the Armée de l'Air planes weren't in flight order. The LW lose a third of its planes in the battle of France but they used them better tactically and strategically, like during the Sedan offensive: nearly 1500 planes (of which 600 bombers and 250 dive bombers, and more than 1200 sorties on a narrow 4km wide target where the German
infantry later crossed the river Meuse) in what was the war's most concentrated use of air power, which resulted in the start of the Anglo-French collapse.
3) Even 1940 infantry could severely harm tanks when dug in, during the Battle of Amiens (20 may to 8 june 1940) two infantry divisions stopped 3 PzD for 15 days and destroyed about 200 tanks or the unsuccessful Abbeville counterattack where the 4°DCR and 2°DCR with some of the 1st armoured division where stopped by 57. Infanterie Division in one of the two biggest tank attacks before Kursk (the other was Hannut)...
4) River crossings under fire are really too easy. The penalty for the attacker should really be huge (even worse for tanks than for infantry), as it was during ww2 even when the US army came with its amazing logistical capability (crossing the Moselle in 1944 was one of the main operational aim of a full US Corps (XX) and they were desperately looking for bridges). Same for amphibious assaults, it took the Allied nearly two years, the Dieppe raid and its disaster and then North Africa to do it right, with considerable amount of investment into planning, equipment, combined armed tactics etc.
V- Gameplay - air-to-ground warfare
1) It's a little harsh to grant planes the same bonus against tanks in a forest and tanks in a plain. You had no IR detectors or laser guiding in 1939-1940 obviously so you relied a lot on visual and line of sight!
2) Medium bombers might need some love, there were hugely used during ww2 and until 1943 quite successfully (after that the fighter could carry almost as much bombs and allied air superiority made them almost useless for the Germans, but for the first part of the war they were much more used (and far more numerous) than dive bombers. Currently they are almost useless except against infantry on the move.
V- Gameplay - air-to-sea
1) Isn't the fighter range over sea a little too long? If I recall correctly it was one of the issues of the Luftwaffe during the Battle of Brittain?
2) It seems destroyers and cruisers take a lot of damage from planes, which sounds suspicious, even more so if you consider that battleships and battlecruisers appear to take less damage, which is not what actually happened during the war where the battleship proved very vulnerable to air attacks.
VII- Oob
Appart from the aforementioned things pertaining to the British tanks, I've noticed the French oob fully misses the Armée française de la Libération (from august 1943), so mostly American equipped French soldiers (iirc they had M4A1 and M4A2 Sherman, some M4A3, M10 Wolverines, M7 Priests for the 3 Divisions Blindées, P40 Warhawks in Tunisa, Spitfires for Overlord, I'm most certainly missing some, but it makes the French option really difficult in all scenarios. I recently saw some pictures of Somua S35 that were used by the Free French in Tunisia from November 1942 too. And British troops also used a lot of Shermans in the 1944 armoured regiments.
That was long. Once more, great work!