Manual conversion magnum

[TerrysTrans]

I have an early 2005 Dodge Magnum that has been procharged and converted to manual, along with other upgrades. The mechanical turnover to manual was easy, but the computer end was hard. Following a guide from Silver Sport Transmissions we were given a PCM pin to wire to the clutch pedal for the clutch safety switch. However, after flashing the PCM to manual it would never start. We even tried bypassing the pedal switch (maybe it was faulty) and giving it the required voltage directly to the pin in the PCM and it still would not fire up. It would key on but not fire, like it was not receiving the signal no matter what we tried. After weeks of trying, we removed the Range switch from the old nag1 and tacked the switch into N, bolted it in under the center console and returned the tune to automatic, and have been able to run it well to get a few good pulls, the clutch broken in, and most of the other mechanical maladies sorted. Obviously, this is not the perfect technical solution, so now that most of the mechanical gremlins have been sorted, I'm trying to get the programming end sorted.
With that, I have two questions: some digging and talking over at silver sport, it seemed some of the early PCMs didn't have the ability to be converted to manual, even if the tune indicated Manual, the actual PCM didn't have the circuit to check for the clutch safety switch - can anyone lend validity to that? (I'd prefer to have the clutch lockout work correctly) Secondly, if that is the case - the neutral trick has worked well for a few weeks of driving to iron out the mechanicals and break in the clutch, I have no issue leaving this setup, but is there more work to be done in the file to ensure proper engine operation as long as the TCM thinks the vehicle is in neutral - are there other neutral protections in place that would prevent the engine from running properly besides the redline limiter? I disabled most of the torque management and copied data from an 09 manual challenger (where the trans came from). It feels good and strong, but it definitely needs tweaking (there's been incredibly helpful individuals on the timing end of things in these forums - with no torque converter and a lot less rotating mass I need work to smooth out general driveability and getting ideal power) and I wanted to poll the experts. Tune attached.

7860 Aa.1(1).hpt