FWD vs RWD has nothign to do with it. Our beloved MX-6/TX5/Probe motor is based on the 2.0 which first showed up in the rear wheel drive 626 of the late 70's. That motor from long ago spawned all the motors which ended up in all 626s and Telstars til '92, the B2000 and B2200 trucks, and our 88-92 MX-6s and the variants of those cars. People have put our motor in those trucks before, and also in Miatas.
It will fit. My friend has a B2200 and he's also thinking of putting in an MX6 GT motor. We parked his truck by my car and looked carefully at both of them for a long time. It (the turbo set up) will definitely fit easy. Problem is the MX6 distributor would not fit in the truck, becuase the back of the B2200 motor is up against the fire wall. On the B2200, the distributor is on the front near the timing belt. So you'd have to use the 8-valve head and distributor on the MX-6 motor. I wouldn't put the turbo on the truck motor, it wasn't meant to be turbo'd. You need a MX6 GT motor to convert to 8-valves. Talk about going backward to go forwards!
Cool thing about the MX-6 motor is it already has the holes drilled to mount either sideways or longitudinally. I also believe you could use a first generation RX-7 bell housing and transmission, as I'm definitely sure people have put the RX-7 transmission in the stock B2000 and B2200 before. This way you'd get rid of the truck gearing. If he want's to go all out he could use the RX-7 rear axle and Limited Slip Differential.