welcome to the forum
you got some decisions to make. personally if i was planning on swapping engines, i wouldn't put anymore money in the 4 banger driveline. but, if you have to fix the trans up now, and can't do the whole motor swap i'd look at swapping the trans to the ax15, which is what came w/ the 4.0, this requires some money to be spent to mate it to your 4 banger, but at least you can still use the trans when you get a 4.0.
here's a link...that should be sticky'd...have i said that yet mods??