Ok, unexpectedly I had some time last evening, so I finally had a chance to look at this. I started a single-player game on Emperor level as the English and played like the first 20 turns. (The first turn took an hour or so, because there was so much new stuff to look at, to read and to learn about...

Can't wait to get the finished Civilopedia...

)
Here is some initial feedback. I just write it down as it comes to my mind, so things that I find great, are mixed with suggestions for improvement...
- I was much surprised to find a Portugese town with the name "New Amsterdam" located in Brazil... We should give that another name, because "New Amsterdam" was a Dutch settlement in North America, which later got renamed to "New York", when the English captured it...
- There is an English fortress located at the border to Florida between an English and a Spanish town. (Can't remember the names right now.) That fortress is filled with two "immobile" Coastal Batteries and a Musketman. Unfortunately the Spanish town seems to have more culture than the English one, so the fortress is located on Spanish territory. Right in the first interturn, the Spanish demanded that I leave their territory or declare war. Of course I said, sorry, won't happen again, and then my "immobile" batteries were miraculously moved to my territory...
Perhaps you should give the English town a bit more culture to make sure that tile is English.
- The time to research one tech always seems to be 6 turns, no matter if you go "lone scientist" or 100%. Is that intended?!
- I really liked the way how you introduced settlers into this scenario by having them auto-built by the Govenor's Palace!
That way the colonies can grow without settlers having to be built. I haven't yet familiarized myself with all the new buildings available in this sceanrio (and many are still undocumented), but I expect you have put many more inventive new features and nice surprises into the game for us... 
- Workers can build Air Fields and Radar Towers?!? Also some units have air defense?!
- Worker costs are much too high. E.g 6 turns to build a road or 20 turns to chop a forest!! I recommend to keep the standard values, otherwise we have to wait ages for something to complete. (Or we would need to build hundreds of workers, which is not in the spirit of this scenario?!)
- One turn is 8 years, which I think is way too long. I only played the first ~20 turns, so the game is still pretty much in the beginnings, but already I have reached the year 1822, so the "golden time of piracy" is long over... I think we need 6 month turns, or even smaller (1 month?). Similarly the time to travel from Europe to the New World is too long. Even the Corvette (using only one movement point for travel in ocean) takes 13 turns, which amounts to 104 years. All travellers would be dead by then...
7 turns and 1 month per turn would be acceptable.
- This may not be a problem in our all-human PBEM game, but I think the AI can't really handle this scenario (or at least some of the nations). Spain looks very powerful at first, but has fallen back extremely on the victory-point graph. Portugal is leading, so they do quite ok, England (me) is currently second, the others are a bit behind but still doing quite ok, but Spain, whom I had expected to be the early powerhouse to which the others would have to catch up slowly, has fallen back and is loosing quite badly. Here is my theory about that: in the first turn I was careless and lost 3 major ships to the Pirates right in the very first interturn. That was a lesson to me and I immediately adopted the convoy strategy replaced the casualties with new ships from London and with enslaved ones and am doing ok now. I assume Spain also lost a significant share of her fleet to the Pirates, but they seem not to have built new ones: Madrid has grown to size 27 by now...! So they can't have built any ships. I assume they simply build dozens of "City Defenders", because that is the "best" unit available...

- But the map itself seems quite "balanced" to me: Spain starts with huge possessions, but only lightly defended. England seems much better prepared for war & new aquisitions, I assume Franch, Netherlands and Portugal are similar, so it just depends on whether Spain manages to keep a large portion of her colonial empire or whether the others "take it apart". With winning chances to everyone. Unfortunately I can't really assess the chances of the Pirates. (I can only say that the AI is apparently helpless against the convoy strategy, so in my current game the Pirates won't have a chance...)
- In the F4 screen there are different leader heads than in the start screen of the game. (The English, French and Spanish Viceroys are dressed like women... They are not transvestites by any chance?!)
- Some concepts are not yet clear to me, e.g. what some buildings are good for, whether all resources need to be connected by a road or whether it is sufficient to have them within the city radius, but I guess that will become clearer, once the Civilopedia is finished.
- Why are there two similar units, Cavalry and Dragoons?? I can't see any reason, why anyone would build a Dragoon: they are more expensive than Cavalry, they are weaker than Cavalry and they cost a population point to build, while Cavalry doesn't. Really, why would anybody build one? Why do we have both?

- It's not clear to me, why some units can't be loaded in some ships?! It seems Cannons can't be transported at all? If that's the case, I vote against it: Cannons should be transportable by ship. And I tried loading a Dragoon onto a Corvette, but it didn't work?! Apparently they can only be transported by Galleon/Merchants?!?! Is this intended?
Ok, more after the weekend (hopefully). But in any case: I liked it a lot! (Even with "only" AI as oponents...) A very different experience from the standard game I usually play. Playing this with real humans should be an absolute killer...
Thanks, Lanzelot
First, thanks for the feedback. This is what I need.
Yes New Amsterdam needs to be renamed. I will fix that.
I will fix the English fortress north of Florida by increasing the culture and decreasing the spanish culture.
Research times on all advances have a max of 6 turns so that all advances can be researched.
The game is 240 turns, each turn =1 month. I forgot to set the game turn periods. I will correct that and post a new Biq file, probably in 3 - 4 days.
I will check on the worker capabilities, I think there was a reason for including those capabilities but I don't remember off the top of my head.
Your comments about Spain are most appreciated. I don't have time right now to test play the game myself so your comments and observation are important. I can beef up spain and make them more balanced. Spain can not build settlers, and must hold her possessions in order to survive.
European warships, can ONLY transport marines and officers. This indeed intentional. other troops can only be transported by merchantmen and other transport vessels. All transport type vessels have weak or no A/D capability. This is intentional so that Europeans will be forced to escort their trade vessels, or lose them to pirates. Of course the choice is yours.
resouces must be within the city radius and connected by road.
In order to increase the pirates viability, I may decrease their unit cost, or increase the european cost, but I will wait for more testing before doing anything for now. The pirates have the capability of producing pirate conscipts by building the PUB. This building auto produces conscripts which are upgradeable to buccaneers. Heres a tip, if the EU is using its stonger fleet to convoy, it is leaving its colonies open to pirate attack

. Also the voyage to Europe is long, pirates can hit and run on a convoy and wear down the escorts.
Coastal fortresses auto produce coastal batteries. 1 battery every 18 turns.
I have fixed it so that workers will be unable to build railroads, airfield, and radar towers.
I will take another look at the cavalry and dragoons and decide whether to keep them both (with changes) or to elimate one or the other.
Finally, the game is designed for multiplayer games, so I tried to skew it for that rather than AI play.
Good post Lancelot, keep me posted.