Welcome SC. Here's some answers to your questions.
1) Vets: The cost of those 3 other warriors was to high for us to pay at the time. We save twice as much gold building barracks to create stronger units so we wouldn't have ot pay those higher unit cost. If we had all those warriors I don't think we would have had all the cash for upgrading.
2) Not upgrading reg units: We were using them as MP and didn't need them upgraded at that point. If you notice when we had more cash readily usable we did upgrade even regular units. Why upgrade a unit that is most likely never going to see battle, and is only there for happiness purposes?
3) The AI considers it a sneak attack. It's a very small rep hit, nothing like a ROP attack, but it does blemish our rep. Right now I think we're pretty spotless.
4) Paying higher prices or gifting does help, but only to a point. Can someone point to the article that states how much gold is gifted before it does nothing to the attitude of the AI? Isn't it something like 100 gold, or 5 times?
5) buy workers: A worker cost around 120 gold. For that, or a tech the AI will give you one of their population, which is a *HUGE* bonus early on. It's such a big advantage in the first 50 turns that it's pretty much "bad form" to use. There is a group of guys who made up some rules that basically limits the human so that the AI won't fall to far behind.
This is one of those rules. The group is called RBC, Realms Beyond Civ. Me personally only follow rules like that when the SG (Or succesion game, the style of game this is) requires it. Bugsy, what's their website?
6) You shouldn't revolt in an SG if it's near the end of your turns. Another reason not to revolt is being in a war where active battles are around your cities. Or if you want to keep "whipping" citizens to remove them from the population of captured cities.
7) Settlers vs Improvments: I can see doing this only if you have a city that can pop a settler every 2-4 turns, and you only have a small area of jungle to clear... unless it's jungle there is no reason to do this... if there is jungle, then yes it can be worth it... 4 turns to build, 4 to move, and 1 to build/disband vs 4 workers for 6 turns.... that's 8 turns to make the workers, and turns they can be improving other things.
8) The rep hit with an ally for killing a civ confuses me too. I'm not sure what's going on with that. No rep hit for destroying a civ, unless with an allience, that I know of.
9) "enough units" is a hard call. COnsider that early on the AI has 2-3 defenders per a city, and add a defender per a difficulty level, and for an era. Usually 4 attackers are enough to ensure you'll take the city, but remember you'll need to leave 1 defender behind and you'll probably loose 1 so you should make sure that you have 2 close for a rear guard per a city. I think we took out Japan and most of the Zulu with a stack of 10 swordmen, but we had at least 1 per a turn being built. As for workers, I like a 2:1 ratio of workers to cities. Most go with a 1.5:1 ration.
10) Any form of representative goverment has EXTREME WW. There is no way to combat it, which is glad we took out our enemies before Republic became avaliable to us.
We can switch after we finish this war.
11) Units forted in a city will get 2hps no matter what verison. It's just hard to spot because you have so many regular units.
Really though, go ahead and test and you'll see it's true. It does take 1 FULL turn to heal a unit in a city with a barracks too.
12) No idea how the order of the AI is done. Is a good thing to test out. Will help determine trade routes.
13) "wooden Spoon" is an award that some folks recieved for having the "lowest score on a varient" for a SG contest we have going on called SG of the Month. You should see that listed too.
I think that's everything.
After the first 20 turns I played the scenario on my own up to 710 AD (kind of a baseline for comparison). I then shadowed almost every turn of the turnsets so the instructor comments would make sense. This has taken a decent portion of the past 17 days. 
This game has helped me a lot as well. 
Any chance you could get those comments on Alerum's turns posted in time for SK to play the next 10 sometime this weekend? 
