Well, it's not really a handicap, most civs have a 255% penalty. There are some exceptions, like Genoa, because the AI usually builds no more than 3 or 4 cities, and has a slow research rate. What I've noticed is that Burgundy has some very heavy modifiers, what might explain why they are doing so badly.
About the savegame: it looks that you've beelined SM. Usually that's not bad, but I think you've skipped some important techs. Monument building is important because of the irrigation. Around 80% of Iberia is plains, and should have farms. Combined with Serfdom (Free Peasantry doesn't have much value IMO), they guarantee powerful cities. Merchant Republic is also something I would recommend. In my last game, playing Hungary, I tried to find the best civics combination for research. I had built the Palacio de Pena, so it wouldn't cost me any time to try it. Results were that Merchant Republic is far more powerful than Guilds. Manorialism is IMO so weak that it doesn't compensate the lost trade route.
Valencia could be improved a lot. It doesn't work all food tiles, which means that it could have grown much larger. I see that you've worked the production tiles before, but to compensate them, you have to build farms all around. Most city locations are chosen well, though Iruna is to small to be significant and Bambaluna would be better if it would be SE.
Some improvements don't remove forests. Windmills were better than mines, because they give food and money and production, and mines only give 2 production. However, windmills remove forests, mines don't. So I build mines only on forested tiles, and windmills only on tiles without trees. Same deal for watermills, a forested grassland rivertile should have a watermills (better than a lumber mill). That's my strategy though, it won't be the best. It might be useful to improve Toledo though, since it has no food to work the mines. Windmills are better in this situation.
Compared to RFC, the land-water ratio is very high, so workers are more important. It is very important to have some workers improving all tiles as much as possible. The starting workers really can't show the full potential.
Your city locations are OK, but you have too many. It would go too far to lure the barbarians to North Africa, but the city adds next to nothing. A city on the south coast near the resources would be better. I see that you have 16 cities, so building another one isn't a good idea. The research bar shows that SM costs more than 30,000 beakers. With 10 cities, it would have been much cheaper. The cities in France are big, but undeveloped, so they harm science rates.
The event log shows 6 anarchies. Every anarchie costs 3 points, so 6 anarchies costs an entire stability level. It seems that both anarchies in 1179 AD and in 1218 AD could have been combined. About your combinations, I'm not sure, 3Miro can probably explain this. Foreign relations are also low. Despite having another state religion, most civs aren't that upset when you meet them. I donate them 10 gold to get the +4, enough to make them Cautios or even (temporary) Pleased. They will sign Open Borders.
Another small trick is that some of the science producers could be transformed into wealth producers. I don't know why, but the science slider has more impact than the production science, so building wealth results in more research AND more money.
Arabia is willing to trade some techs. Tech trading is very important in the early game. Research cheap techs (3 turns to research), and sell them to rich civs, especially Frankia. Byzantium is also very happy to trade techs, so if possible, send out a scout and try to trade something. Trading resources may work too. Currently, you've 6 wine, and you only need one. The Vikings have 13 gold left, more than enough to buy something. The AI changes their gold/research rate very often, so while they sometimes have nothing to trade, the next turn they have lots of gold (Byzantium, Frankia). Trading maps is a good way to get new contacts, and some money.
I hope this helps. It's a quick observation, not a detailed strategy guide but it may work in general. I have to admit though that you just had some bad luck. Venice has more cities than they usually do, these cities in Russia seem to be very important. I've only seen Moscow collapsed once or twice, so it is certainly not common that Venice is that strong.
EDIT: Wasn't the mod supposed to end in 1800 AD? Nick's screenshot says that it ends in 1760 AD. That might explain why the Dutch start in 1540 AD, AFAIK they should start in 1580 AD. Possibly that's why the UHV's are messed up, the date is simply wrong.
. But when I captured the required city I didn't get a bonus, was I supposed 2? Arabia had just collapsed, would that stop it? 
. The assembly line building also seems to have problems, i've researched the tech but can't build it 
?
. I installed the feb 14th version and I could load the game again, but the UHV didn't work again.
. I will look at it, it looks like a mismatch between the map and the exact location of the Dalmatian coast and mainland Greece.
