The mid range miss you have is a problem. The rotary should be smooth as glass. The problem may be that it is running a little lean in this point. That would make a miss and compound your exhaust gas temperatures.
The exhaust on a rotary is EXTREMELY hot. Hotter than any other car. 1600-1700 degrees under rpm/load is normal. Your upper pipes glowing cherry red under rpm/load is actually normal. On my car, even when running with enough fuel (not lean) probably the first 8-10 inches glowed red, then cooler from that point back. I am assuming your speedy is rear engined. That would put the exhaust ports on the driver side. I ran my car with a VW "stinger" type exhaust only with a glass pack insert that coupled short headers to the stinger and straight out the rear. Don't do that. The rotary exhaust was so hot that it melted the fiberglass insert in the first 10 miles and made little glass puddles that dripped in liquid form out the exhaust. Then I had no muffler at all... And rotarys are also the LOUDEST engine ever built. If it is possible, run the water pipes on the passenger side, exhaust on driver's side only. The muffler will be problematic. Probably best solution is the supertrapp type system, it will live with a rotary and in your confined space, give you some type of exhaust. Be advised, it will be extremely loud under throttle, but not too bad at just idle.
Also, regarding the miss, make sure the trailing and leading spark plugs wires are not reversed. They are marked T and L on the rotor housing.
Under no condition should this engine overheat. My car was very picky about the coolant adding system, I had to effectively, "burp" the radiator as it was lower than the engine. Otherwise, I got an air lock in the radiator and the car would get hot. Make sure the thermostat works. I had one that was stuck. So I removed it. It overheated worse without a thermostat than with the sticky one.
I know you asked for an unbiased opinon and I'm a rotary nut so I'm biased. But it would likely take alot less work to fix what is wrong here than to remove all of it including the radiator and start all over. angela