you should be able to get the tranny included with the price you pay for the package also, with the auto trans, you kinda messed up there but it shouldnt be that hard to do a auto to manual....
also here is a place right here in tampa that sounds pretty good, i don't have any experience with them but they sure look like they know what they're doing...

http://www.deepsouthhybrids.com/motorswaps.htm