i would recommend an 04 manual trans 2500 Dodge ram PCM. You do not have to worry about limp in mode with a manudal trans controller. A truck engine will fit in an a-body. One concern is the back of the intake is basically resting on the firewall/bulkhead. The alternator and compressor will clear the hood though. The car manifold is suppose to be better flow, and the no spark plug wires looks a little bit better on the later cars.

Good luck...

I have no experience with the MDS on a swap, so I cant give any advice there!

Justin