well, I doubt you'd be able to rebuild the 4R real well. There are a lot of tools necessary and experience required. Talk to Darrin and Dirty about that one. You have let us know what price range you are working with. A manual swap is very doable if you have the time and patience. Is this your Daily Driver?
If you want a transmission that will actually last, then get one from Darrin, you might as well get an upgraded Torque Converter if you have the money. Buy an entire tranny from darrin, get a marauder or Dirty Torque Converter (search about Dirty), and drop your motor from the bottom, unbolt it, bolt up the new one, throw her back in there.
2.25" True Dual Catless DI/DO Magnaflow Exhaust, Eibach Springs, Addco 1 3/8", J-mod, Viper 791 Alarm, Clarion 855 full color touch-screen, Directed 2400 amp
, 2 12" CV Strokers with a custom ported box, K&N air filter, 180* T-Stat, Xcal2 SCT TUNED BY LONNIE
17 x 7.5 (245/45/17) Chrome Cobra R's, 17x9 in back(275/40/17)
DOHC sitting in the garage
Teksid 2v plans?!?!
Tranny Cooler, Dual Remote Oil Filter waiting for install