98 4.6 trans. questions...HELP!

now that i got a motor out of 98 gt i found out my auto in my 99 wont bolt up so now im on the hunt for a trans, can someone help me and tell me what to look for? for a 5 speed i would need a T-45, right? what about auto? oh yeah and how hard is it to install a manual in a auto car?

thanx,
ryan

PS-this is alot more work than i thought :( but im tryin to pull through!
 
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