Transplant 13B to 1st Generation
The GSL-SE's came with a FI 13B. And the 2nd generation RX's have the same basic motor, BUT, I know they mount differently.
How many parts do you have to change to fit that motor to the early car?
My old '79 12A RX7 is beginning to get tired and I'd like to fit an '89 or later 13B into the car. The chassis is all seam welded and has a welded in cage, '84 struts, GSL rear, '80 front brakes, a 22 gallon fuel cell, fiberglass hood, Eibach/Tokico suspension and about 75 feet of braided stainless plumbing. Nevertheless, it deserves more than the 12A can give it (and so do I).
Impressing me with what must be one kick-*** '79! I checked the MazdaTrix catalog for info on your engine swap, but they only give details on installing the 2nd gen 13B's into a 12A 1st gen. Maybe you should call them for their ideas. They're remarkably willing to give out advice. They have any appropriate mounting adapters you might need. Now if you'll excuse me, I'm off to find a junkyard with an '80 (for the front calipers) and a GSL-SE (for the rear disks).
My advice is to simply, go out and buy a nice '89-on 13B, and then go to Mazda Motorsports, and buy an '85 GSL-SE oil pan (~$35.00) and gasket. That's about all you'll need. The 12A front cover can be swapped over to the 13B, which gets you the old style front motor mounts. The stock motor mounts can be slotted to mount the front of the engine. The 12A distributor can be used in the 13B, but if you can get the entire wiring harness, and ECU, then you can run the 89-on engine exactly as it came from the factory. You'll also need an electric, high flow, high pressure fuel pump, if you go this route. The stock fuel lines will probably suffice though, unless you build up the 13B.

13B into 1st Gen
I had an '88 13B installed in my '84 GSL-SE. You need to change the oil pan and the front cover only.
(Not surprising, since they both have a 13B - FAQMaster)

13B into 1st Gen
I'm considering doing this swap too and am compiling info on the topic. What I've found is you can use any 13B, whether it's from an Rx-4, Rx-7 (GSL-SE 84-85 more restrictive EFI), or Rx-7 86-91 as long as you use the front cover off your 12A so you can use the original motor mounts, alternator, water pump. Don't know if A/C will bolt up as it's bracket bolts to the block and the 13B is longer than the 12A. You'll also need to use the oil pan from a 84-85 GSL-SE. Your 12A distributor will swap over. I'd reccomend upgrading to a three row radiator from Mazdatrix or using a 13B radiator. The block will bolt up to the tranny no problems.
Intake is up to you. You can buy a Holley 600cfm or Mikuni 45mm from Mazdatrix, Use a Rx-3 carb, enlarge your stock carb, buy a Dellorto 48mm used (Racing Beat doesn't make them anymore) or upgrade to 13B EFI which is really your best bet. It's used (cheap) and easy to get repair parts for. Or you can buy a Haltech or Motec unit for $3000 and $1500 respectively.
I haven't heard of someone using a 92-96 twin-turbo 13B because there's a lotta smog/electronics/crap on those engines that you'd haave to sort out/take off. Also those engines cost a lot of money.
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Timing
Location of the Timing marks
The timing marks are stamped on the pully groove closest to the engine block itself. about 1/2" apart, may be red/yellow marked.
To find marks, look down between dist. and alternator pulley.
By advance, I meant that some t-lights have a dial that allows for adjusting the spark advance, however is not compatible with the Rx-7 ignition system. If the light has dial, keep at 0 degrees.
Correct plugs are NGK BR8EQ-14 models. Unless timing has been messed with, rotarys do not normally require timing adjustments. If timing off lots, hard to start, very rough idle, etc.
I suspect ignition problem such as plug type, distributor cap/rotor, ignition wire set, shutter valve, bad leading ignitor, bad anti-afterburn air pipe. I am assuming the firing order is correct.