Just so happens I've done this swap a few times now. There is plenty of info at sorscode.com
Sorscode: Performance & Swap Specialists | Performance Parts, Muscle Cars, Aftermarket Wheels, Aftermarket Exhaust
To answer your questions:
the 3.8 AODE will work, but will require the little black control module found behind the glove box on 94/95 5.0 AODE cars. Also, the bellhousings are integral to these transmissions, they cannot be changed. But the bolt pattern on your sixer is the same as 5.0/5.8's
I don't think the lightning ECU will work as is, would probably require extensive repinning. A 94/95 5.0 ECU would work just fine with your 5.8.
Let me know if you have any other questions, these swaps are fun and I enjoy helping folks out with them.
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1994 GT: 5 Speed conversion, BBK Shorties, O/R H, Flowmasters. Rest bone stock, even has air silencer!