If you convert to a carburetor on the FC engine, it simplifies the swap significantly, but I can't really recommend it because carburetors suck. (Yeah, that's right, I said it.
) But I can't really help you with the stock EFI swap-over because I've never done it. Hopefully someone will chime in who has.
You'll want to take the motor including the alternator and whatever other accessories you may want, wiring harness, ECU, sensors, and you'll probably want the coil packs and maybe the fuse box (again, I've never done the EFI swap). You can grab the transmission if you want, but you can use the stock 12A one, too (you'll be using the rear of the 12A tranny either way). The FC trannies are geared a little taller; Mazdatrix has the gear ratios on their site if you want to look at them. You'll use the FC flywheel and clutch setup. The '89-92 (S5) engines are better than the '86-88 (S4) engines, but take a few extra steps to install in a first-gen because of the electronic OMP (you'll be using a mechanical one and will have to fool the ECU into thinking the electronic one is there and working).
For the engine mount, you'll be putting your stock 12A front cover on the 13B. The 12A OMP only has two outlets instead of four. This is okay; just block off the oil injectors in the 13B's rotor housings and run the lines to the ones in the intake manifold. Or you can tee the lines apart and use all four oil injectors if you prefer. If you have an S5 engine, you'll need to either fabricate a rod to lift the OMP arm when the throttle is opened, or take the easy way out and just wire the OMP arm to the 9 o'clock position. The S4 engine should already have an OMP lifter rod.
You'll also need a GSL-SE oil pan and any one of the following: a Racing Beat front mount bar, a GSL-SE crossmember, or some fabrication skills to slot the holes on your stock crossmember and front mount bar. The former is necessary because the FC oil pan will not fit in a stock first-gen chassis, and the latter is needed because 13Bs are 20mm longer than 12As.
Oh, and of course you'll need to modify your exhaust to fit a 13B. Or better yet, replace it with something that flows better. Not sure if the stock FC ECU relies on the O2 sensor being there; if it does, you'll have to add it to whatever exhaust you use.
Another issue is the auxiliary port actuation. S5 engines use the air pump and emissions rack to open them, S4 engines use exhaust backpressure. That means that if you use an S4 engine, you're going to need to add a backpressure sensing tube to your exhaust if you want to keep the auxiliary ports functional. This can be a problem with high-flowing performance exhaust systems because they don't have enough backpressure to open the ports. Kevin Landers has a writeup describing how to actuate the auxiliary ports electronically, eliminating the need for a restrictive exhaust. It can be found
here. The other option is, of course, to just wire them open.
If your car is an '83-85, it's equipped with a "beehive" oil cooler, which uses coolant. You CAN use it on a 13B with some modification, but don't bother because it sucks anyway. Get rid of it and convert to a front-mount oil cooler. You can take this off the FC or an earlier rotary chassis.
Next you have to address the fuel system. Your stock fuel send line should be enough. The stock return line is only 1/4", which may or may not be big enough to keep your fuel pressure in check. You'll need an EFI-style fuel pump. A Walbro 255 (p.n. GSL392) is cheap and will flow far more fuel than you'll ever use without a turbo. An MSD 2225 pump would work well, too. Don't forget an EFI fuel pressure gauge and EFI-rated soft fuel hose.
Then rig up an air filter and that's basically all there is to it. You may have to play some games to get the tachometer and stock gauges working (not sure if the FC engines use different water temp or oil pressure senders; you may have to swap your 12A ones over).
Here's some more recommended reading. Especially take a look at the emissions removal guides if your region allows it, and the pulsation dampener elimination (the PD is the cause of a lot of FCs burning to the ground).
http://www.rotaryresurrection.com/2ndgen/techmenu.html
Let me know if you have any more specific questions.