Yeah, I think it can be changed to +1

instead of +2

. I'd also make it obsolete with printing press (makes sense).
In fact every religious building providing science should take a hit in the later part of the game, even before Scientific Method. I'd have, as proposed some weeks ago, a "printing press" related, non-religious building providing some science instead of the scriptorium (or compatible, lessening the scientific effect of the latter). Even increasing the effect of Universities.
By the end of the Middle Ages the "researching" effect of monasteries declined quickly.
Now apart from that, I remember it still is to be discussed the exact effect for the remaining wonders, which I should begin coding this weekend:
Belem Tower: trade route boost (although Magellan's Voyage has that already), enabled by Shipbuilding (I'd put it a bit later)
Tomb of Khalid ibn Al Walid: same as Statue of Zeus (Arabic Knowledge + Chivalry)
The Golden Bull: enables all religious civics (Divine Right)
Kalmar Castle: replaces Pentagon (Professional Armies)
Escorial Palace: suggested to give an economic boost; I'd put it as complementary to bureaucracy, that is, +50%

, +50%

in its city. The Escorial is the great spanish monument from the time of Philip II; he was known to have spent years just signing papers everyday as the spanish bureaucracy was the biggest one in all Europe back then.
Temple Mount: jewish quarter in every city? I'd prefer it to replace the jewish shrine (prebuilt at Jerusalem) and have another wonder with some limited economic effect but also with the same "expanding judaism" effect as the shrine. It could come with a late middle ages tech.
National Bank (?): same as Wall Street, yes or no?
which Palace graphics to replace the current ones?
and something to replace the "Academy" (name and concept not appropiate, IMO) and "Scotland Yard" (Tower of London proposed), to be built by great scientist and great spy. I can't remember now, but the Military Academy can only be built by a great general after after Military Tactics, right? (unrelated issue: with a mod about the Middle Ages and after, the word "general" doesn't strike me as suitable)
Edit: I'd also welcome comments about the last wonders introduced, specially L'Enciclopedie project and Marco Polo's Embassy, which weren't discussed here before. I think some wonders are overpowered in relation to others, but it's an usual thing in Civ4, I suppose.
And about the splash images ("movies") for them. You can see them just clicking in their folder. Only need Gimp and the DDS plugin, for example.