rear rotor seems dead at idle
 

I've got an '88 TII with nothing but the shortblock stock. Me and my buddies made our own ECU. Right now we just have the spark advance locked in around 5*BTDC. There is a MAF that talks to the ECU and we control the mixture with a potentiometer for the time being.

Here is the problem:
it looks like the front rotor is running great. we can get it started and it does the "wop wop wop" thing sometimes, and sometimes it just hums at an even frequency (mainly after it has warmed up). We used an IR thermometer to check out header primary temps. At idle, the front rotor exhaust pipe is around 350*C and the back is at around 90*C!

I don't have enough experience with rotaries to acoustically determine if both rotors are running, or if only the front is, but the thermometer definitely indicates that the back is not firing for some reason.

We are only running leading plugs, and we have tried swapping the ignition coil wires to them, and the back rotor is still the problem. We have swapped primary injectors, and the back rotor is still the problem. We have swapped injector wires, and it's still the back rotor.

We have swapped out both spark plugs with new plugs many times, and it's always the back rotor.

Does anybody have any suggestions for what might be the issue? We are at a loss on this one. Is this a common problem with a bad apex seal or something? Is there some other common cure for this issue?

Has the block ever been rebuilt?

Could even just be a stuck seal. Start with seafoam.

The motor had been rebuilt about 5,000 miles back by the previous owner. elegidly it ran in a car just fine for thoes 5,000 miles.
I just discovered some new clues though. We shut the fuel pump off and the engine continued to run on the front rotor only for about 10 minutes. Now I am thinking I've got lots of crap in my injectors which is resulting in at least one of the front rotor injectors sticking open. I am wondering if the debris could also be casuing the problems with the back rotor. I'm going to take the injectors out and do some testing tomorrow.