This is a project I've thought about for some time! 
Building a custom left engine mount is easy to do, the right not so much. 
The stock RX7 mounts are at best 'floppy', I dislike them so I used polyurethane 'tee' bushings from Energy Suspension to make my mounts. I can get you pics of how mine were done if you need ideas.
If you need more flexibility of engine position than the whole stock Miata powerplant frame thing gives you, the RX7 shifter can be moved forward up to 4" easily and I think the Miata's can as well. The Miata PPF can also be easily shortened as needed. I'd dtry to scoot the engine back so the front pulley is in line with the front axle centerline, that shoud be pretty easy without a lot of firewall pounding. The only thing which might get in the way is the clutch slave cylinder/clutch fork.
I have used two of the Racing Beat header kits, they are reasonably priced and work well. The best thing is they include 2" OD .120 wall tubing, the 16 gauge stuff in the cheap aftermarket headers can burn through QUICK. You really don't want rotary exhaust blasting into the engine compartment! The stock RX7 manifold is heavy and it strangles the engine, there's an easy 20 HP in a set of headers even if the primary tube length is not ideal (it's best between 24 and 27 inches).
About easy and low budget engine management: MS etc is certainly doable, but here's the easy way: use a S4 ECU with a S4 front cover and mechanical oil metering pump. The S4 front cover is an easy swap. The only mod you have to do is grind or cut away about 3/8" of a water pump stud boss on the S5 water pump housing, otherwise the whole thing is a bolt on deal, you can even use the S5 oil injection lines. A word of caution: be VERY careful of the eccentric shaft thrust bearing! It's a needle bearing with .0015 of end play and can easily be knocked out of position if you aren't careful. The best way to do this is with the front of the motor tilted up and the flywheel wedged forward so the eccentic shaft can't slide toward the back of the motor. If the transmission is still on the engine, you can use the clutch mechanism to wedge it forward and I've done it in the car by using a 2x4 between the seat and the clutch pedal. Then remove the pulley adapter from the eccentic shaft and remove the front cover, etc.
While you are at it, there is a temperature controlled thermostatic 'pellet' which keeps oil from being sprayed inside the rotors until the oil temp gets high enough. Those things fail in the closed position, causing the rotors to get too hot inside and roasting the oil control O rings, leading to oil consumption which must be experienced to be believed. Atkins Rotary has a blockoff kit, or you can stack 3 8mm ID lockwashers on the shaft of the stock one when you reinstall the eccentric shaft bolt, this does the same thing.
The wiring diagrams etc for both management systems are easily found on line and I happen to have a spare S4 ECU. The S5 'inline' air flow meter is compatible with the S4 ECU, that's what is on my car now. Otherwise, the only sensor you would need to replace is the throttle position sensor (use an S4 piece, you have to make a simple flat metal bracket); the air, coolant temp, etc sensors are the same from S4 to S5. The S5 TPS's are much sought after (hint, hint: budget recoupment!). I made a cable to operate my OMP, using bicycle brake cable casing and wire. If you go this route, add a compression spring at the OMP so that when the OMP is wide open, the spring allows the throttle to open a bit further without bending anything. I can shoot you a pic showing how I did mine if you need it.
The '6 port' actuators run off of the exhaust air injection pump and do make a noticeable HP difference at higher RPM, so you need to leave that in place. Or, you can use an RPM activated switch and one of those cheapo air pumps for a standalone setup (that's what's on the Jensenator at the moment). The weird thing about them is they run off of PRESSURE, not VACUUM. Atkins Rotary has 6 port valves which are shaped for better air flow and again these make a noticeable difference at high RPM. They are something like $70 for a set.
The S5 thermostat housing is plastic and they are known to break. I used a FB metal one, redrilled the two original holes and welded a tab on for the 3rd bolt hole. Took a load off my mind! Don't run the engine without a thermostat, the 'internal bypass' will prevent coolant from getting to the radiator and make it overheat. Rotaries do NOT like overheating! You can also use a S4 water pump housing, this will give you an aluminum thermostat housing with a high 'fill point' but it may not clear the Miata hood.
