Please tell us more about your mods and custom speeds.
Well, currently I'm running the following adjustments to Marathon:
I also adjusted the Pantheon/Great Prophet rates up 400% (40 to found first pantheon, 20 each additional, first GP at 800 with 400 increment) and extended Peace Treaty length to 30 turns.
I removed all Free Tech/Social Policies replacing them with other benefits (currently free Great People, but I'm still testing to see if this throws off GP rate too much, if so I might adjust the GP rate down to compensate or come up with another worthy bonus to replace free tech/SPs).
I'm playing with no Ancient Ruins (I'll get to adjusting their outputs later) since free tech, unit upgrades, free pop/settlers, huge culture/faith boosts - and to a lesser extent even large amounts of gold - gives the lucky finder a HUGE boost over other empires early in the game (when your first tech will take about 40-50 turns, stumbling across a free tech in half a dozen gives you a tremendous edge over everyone else).
And I swapped the bonus food from Granaries with the Food Kept After Growth from Aqueducts to slow initial growth and extend Ancient era slightly (had a side effect of making Tradition finisher give free Granaries, so I'm working on a rebalance for it since a free Granary in 4 cities is basically just 4 less maintenance a turn - by the time you complete the tree you will likely already have built them - and not that special)
Had to adjust unit maintenance to avoid empires going quickly bankrupt since the game length is far longer than standard marathon pace and I made all civilian units - settlers, workers, workboats, Great People, missionaries, inquisitors - maintenance free (still testing those values since the occassional empire can have outrageous income mid to late game - such was the case with Ethiopia when they pursued Diplomatic Victory, I was hard pressed to stop them because they had an incredible income compared to mine)
Modified some of the civ traits to avoid them unbalancing a slower paced game (for example I removed the Science bonus from generic Citizens from Korea so they only get a bonus from true Specialists and makes less of a major tech gap early in the game but they still retain a competitive edge from building wonders and specialists) - oddly enough I didn't need to adjust France since slower research pace means less cities you can manage and the minor culture boost doesn't make them a massive runaway (they do take the culture lead early, but that SHOULD be the case of a UA, it just shouldn't mean insta win).
Outside of game speed related changes, I'm incorporating other changes that make the game more enjoyable for me (quite a bit from CIVUP/VEM such as deserts/snow taking 2 move and promotions to counter it and I'll be working events in eventually) including:
Made barbarians a bit nastier (150% bonus vs cities, the ability to embark across oceans from the game start and their naval vessels can also limp through ice tiles at 1 tile per turn - currently trying to figure out how to get them cross mountains now that Can Move Impassable doesn't work since the Carthage UA) so even though they don't heal you have to keep an eye out for them and I usually play with them Raging. They still have a cap on xp (although a bit higher than standard, 100 vs 30) but plundering camps has always been its own reward and with Honor they become even more valuable (not to mention certain Civs have UAs that make them worthwhile - Aztecs, Germany, Ottomans, Songhai... even Celts now).
Extending Recon units past Scout
Adding in a line of civilian promotions - they currently only earn xp when first produced, it's granted by libraries, universities or public schools as well as Collective Rule policy in Liberty
A few new units (my main one is a truly late game unit - Combat Engineers with Globalization, they're basically workers with a 65 Combat Strength, extremely weak vs any Future era, who can earn Recon promotions and duplicate any Build of a Worker but can move through ice and paradrop to access regions otherwise inaccessible to standard workers - I started incorporating them way back before G&K cause I often found otherwise inaccessible locations with resources, especially ringed by mountains or along the poles)
Modifications to some buildings (Univeristies give less science from jungle but also offer some for other areas like Marshland and Sea Resources making them more useful worldwide instead of just in heavy jungle areas... gave a bonus to GG rate to Heroic Epic and added the Morale promotion to a few other National/World wonders - I always found myself trying to build ALL my units out of whichever city had Heroic Epic because of a free promotion, having 3-5 cities to do so helps my OCD a bit
and was a better solution than making the promotion instantly apply to all units akin to Great Lighthouse).
And a few other tweaks still the works (portaging crews for workboats/Great Admirals to transport them across land to different bodies of water, for example... still rather buggy because you have to swap back to workboat BEFORE embarking the crew and swapping from Land to Sea units will not always put you in the adjacent water tile - often find the unit teleported to the nearest coastal city so I can't get the workboat to a resource blocked by ice from the city as I'd hoped right now...).