I want to upgrade some of the old Civs from Civ4 Vanilla. Now I read some where that there is a program that lets me take the file and compare it to others to see what im missing in the code. any idea?

A free tool for file comparing is WinMerge (http://winmerge.org/index.php). Simply a great tool. Wouldn't know what to do without it.

From Vanilla to what?

I made this to convert xml from vanilla to warlords: http://forums.civfanatics.com/showthread.php?t=211975

I don't have BtS, but the script reads the schema files, so unless those have changed radically it should work for that too. It only converts forward since it only adds tags. I just didn't bother coding in handling "downgrading" mods.

I've seen it stated a lot of times by the well-known modders here that converting from vanilla/warlords to BtS is a *lot* more time consuming than from vanilla to warlords.

Generally, people are rewriting from scratch, I think.

Rewrite from scratch or wait for somone to make some really powerful upgrader. There are a ton of changes. Personally I'm going from scratch.