After eliminating everything else it should be obvious what the problem is....
Apparently you're chasing the worst kind of electrical issue... An intermittent. Could be anything. Relay, open wire that when flexed makes contact and works for awhile or an intermittent short. If moving/reseating the PCM ground always allows the car to start I would trace that wiring (test continuity end to end) and try jumping around it to see if that takes care of your symptoms. If it does determine if the wiring is at fault, connectors, eye terminals, etc. (I still have a hard time believing the PCM could be intermittently working. To be sure you'd likely have to take it to a dealer to run tests/check for any codes).
If symptoms do not improve I would follow the trouble-shooting procedure again in the manual and look at all components that are supposed to change state during the starting cycle (switches, relays, etc). Is everything (voltages, grounds) available where they're supposed to be for the car to start? Does the Clutch Position Switch work yet? Also look at the SJB circuit.
This might be repeating the obvious but in case it helps it could be worth another look.
Pin Point Test A: The Engine Does Not Crank And the Relay Does Not Click:
Normal Operation: In normal operation, voltage from the BEC is supplied to the ignition switch through circuit 1050 (LG/PK). When the key is turned to start that voltage is supplied through circuit 1522 (DG) to the SJB.
For a manual (when the key is turned) voltage from the SJB runs to the CPP (Clutch Pedal Position) switch via circuit 32 (RD/LB). Then when the clutch pedal is depressed, that CPP voltage is routed to the starter relay coil in the BEC. At the same time ground is supplied from the PCM through circuit 1419 (LG/YE). (That should energize the starter relay).
When the starter relay is energized, voltage supplied to the relay switch is sent to the starter motor solenoid through circuit 113 (YE/LB). B+ is present at the starter through circuit 2037 (RD) at all times.
End
If relays are not closing and/or voltages and grounds are not present where/when they're supposed to be you have to determine why (open, no ground, relay not completing the circuit, short, etc). Easy to test the relay using another of the same type. For SA, even components you've already replaced can be compromised. Should be fairly straight forward to test for grounds and voltages at the BEC, SJB & CPP.
Additionally, might help to search no start conditions online for similar problems, what failed and fixes/pointers to nail down what went wrong.
If nothing pans out could be worth an hour of troubleshooting at the dealer. I know not ideal and even in my own case all the dealer did was help me eliminate a couple of items; not fix what my problem was.