Is the car still not turning over? Because if you are lacking spark and priming in the fuel pump then replace the main relay. (also, I've never been able to hear my main relay turn on- it is a plug so Im not sure how you'd hear it(?)) Also, take out your ecu and open it up. Just do a check that you did not fry it. Also,unplug your ecu and try a different ecu. This may help. A lot of things trail back to the ecu with problems.
I didnt read anything about your ignition system being upgraded...but if the ignition system and ecu are not compatible then the car wont run either. If the wiring is messed up from the ignition system to the ecu that would affect your rpms. Check that wiring has been done properly and again- check the combatibility of your ecu to ignition system. I saw that you said you replaced the fuel filter. But did you replace the fuel pump as well?
And finally- check that the injectors are not stuck fully closed. A stuck closed injector will not click or send out any fuel. Check that your pulse width is not all the way down to 0.
When your car WAS running all shitty...it may have been one of your sensors that made it run bad...check or replace them (crank ref signal, map, tach signal, maf ect)

My car had the same issue...so i had to do the whole trial and error thing. After replacing a few items and checking EVERYTHING- finally I found out it was the wiring to my ecu. Good luck- i hope this helps get your car running again