I plan on Slipstreaming SP3, IE7, and WMP11 to a XP Home SP1a disc. I already have the KB947864 hotfix for IE, are there any more that I would need? I saw some other people pointing to one for WMP11, is there a hotfix that isn't installed with SP3 for WMP11?

For IE7 you can use OnePiece's addon, and for WMP11 you can use Boooggy's WMP11 Slipstreamer. On the Slipstreamer site there is a list of hotfixes to download.

If I add all of the IE7 hotfixes and WMP11 hotfixes, will that cause any problems with SP3? Will the most up-to-date files be kept?

Well Ive integrated IE7 and WMP11 into SP3. I havent seen any problem.