Sorry to read of your troubles.
Stabbing wildly in the dark and some suggestions:
I have heard that some flywheels can be put in out of phase, basically 180 degrees out, although not sure which ones, it was the first question asked to me when i had a cps sensor go down when i swapped flywheels to which i had similar problems, running rough as hell and would only start with foot on the gas, fortunately it was literally the sensor on mine, although we did take off the gearbox to check the alignment was correct.
I am also sure i have read because the throttle bodies are fly by wire, they can need resetting if removed, especially if your battery has gone funky whilst off.
Other than that and i have no idea who you have taken it to, but imho take it to a specialist, someone who is fully up to speed on this sort of car, Horsham, Abbey, Kaizer Motor Company.
I would also suggest with a car like this, you need an HKS twin spark, they were a life saver on Rx7's.