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We don't discriminate here...the 2.3 used in that 'Stang is the same one used in our trucks. And besides, you have a BII so you're in!
First of all, you don't have to have a code scanner to check the codes yourself. Sure, it makes it a bit easier but you can still do without it. Here's how:
http://fordfuelinjection.com/?p=13
The other thing to check is fuel pressure. You check it at the Schrader valve on the fuel rail. It should be in the range of 35-45psi.
It's most likely something pretty simple, but you can drop the plan of putting the tranny behind your 2.9, it won't fit. The bolt pattern looks similar but it's just different enough not to work, and besides, the starters are on opposite sides and the transmission input shaft for the V6 is longer.
Is that a 4X2 BII you have?