Karthin

I have been having an immobilizer issue, that appears to be electrical, for over a year. I am finally asking online for help as the local Honda dealership can't help. I'm not in an area with reputable performance shops where the closest is about 100 miles away and I am nervous driving it with its current problem.

Car mods, mostly focused on items affecting the electrical system:
Supercharger (and intake, headers, and exhaust)
Apexi VTEC Controller
Turbo timer with override wired to e-brake
Alarm
Guages

Problem:
Immobilizer activates randomly while driving. The car might work a week, it might work an hour; but its going to happen. It continues driving; but when the vehicle is turned off, it won't start again with either the primary key or the valet key, no matter which one is used.

Behavior:
Once freshly reprogrammed, the car will start normally, with the expected immobilizer flashing sequence and then turn off.
Eventually at idle the immobilizer light will turn on and flicker. Coincidentally and highly likely related, the VTEC controller experiences the same flicker
Revving the car up above 3-4k RPM makes the immobilizer light go solid and then go away after letting off until the car returns to idle.
Holding the RPMs steady around 2k results in the immobilizer blinking steadily like during start up (and will 100% trigger the immobilizer).
While driving, if the imobilizer light is off, turning on the AC likely results in the immobilizer light coming on

Steps taken so far:
ECU and Ignition switch replace (before I saw other electrical symptoms)
Battery replaced
Alternator tested good - made like 90 amps at 13.6V

My guesses:
With all this considered, this is clearly (to me) an electrical issue. My guesses are that it is either an issue with wiring, the voltage regulator, or the alternator. Could an alternator pass an alternator test and still be responsible?

Any ideas would be greatly appreciated; thanks!