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Truck in sig line is intermittingly not wanting the start with out moving the gear selector around a bit. I'm thinking neutral safety switch but not 100%. Anything else ?

History of the truck. Truck was purchased in 2002 with 43K miles. Engine and transmission were stock except for a K&N drop in air filter. Early 2003 installed a PowerMax programmer from TST which displays boost, transmission temp, and EGT. Late 2003 installed a PacBrake, TripleLoc (three clutch disk) torque converter, and HP valve body from TST. 2007 spring had check engine light and intermittent hard starting local diesel shop diagnosed it as a fault between primary and secondary computer and cleared the code (don’t know what the code was). They checked my fuel pressure which was around 10 at idle and much less under static 2400 rpm throttle. He advised getting a new fuel lift pump. Aug 2007 installed a fuel pressure gauge, engine oil temp gauge, FASS 95, and rebuilt VP44. Fuel pressure 17 at idle 14.5 at WOT. July 2008 installed MagHyTech Double Deep transmission pan and 14CM turbo exhaust housing on the HX35. December 2008 began experiencing hard starting when hot after sitting shut off for more than 5 minutes. Truck had check engine light P0336 CKP sensor. Took the truck to Lithia Dodge in Anchorage who kept it for a week and said they couldn’t find anything wrong and the CKP was fine. I told them to change it anyway. They wouldn’t do it and told me that I had to remove the Fass 95 and any other aftermarket items installed on the truck (Pac brake, converter, valve body, programmer, etc.) as they didn’t understand how they worked or could affect the diagnostic equipment. I told them where to put their dealership and where I would not purchase my next vehicle. Took the truck home and changed the CKP with one from Cummins. Hard starting problem solved. I Installed 18” of clear fuel line at a high point before the vp44 to be able to check visually for air in the supply fuel line. (I have never seen any air) July 2009 began experiencing hard starting when hot and sitting more than 5 minutes again along with stalling when shifted into drive from park or neutral. I Cleaned the Map and IAT sensors. No joy. I installed a set of Edge 80 hp injectors, new connector tubes and O rings, and a CoPilot transmission controller for the PacBrake. I also soldered all connections for the PowerMax programmer and CoPilot. Starting and shifting problems went away. Aug 2009 installed BHAF and 4” MBRP exhaust. February 2010 Shifting and hard start problems returned. Truck starts fine after sitting overnight and completely cooling off, but stalls when shifted into drive. Engine does not idle smoothly seems to hunt for a idle rpm to settle into. If left idling for a longer period (30 min) the hunting grows worse until the tachometer is swinging 100 or so up and down. Revving the engine settles the hunting down a bit but the hunting continues. When the engine stalls after shifting into gear it usually re-starts on the first try. The stalling is worse when the truck is cold than when hot. The restart problem is worse when the truck is hot than when it is cold. Bringing the engine rpm up to about 900 will usually prevent the stalling when shifting. Sometimes after stalling several times and then getting on the road just idling along at 5mph or so the engine will suddenly go rumph, rumph, rumph, rumph, rumph quickly like it’s going to stall then catches itself and revs a little each time to prevent a stall. I have checked the fuel return line, rear banjo bolt, and all fittings and clamps for fuel leaks and found none. I have replaced the VP44 fuel return check valve. I have re-calibrated the APPS memory. March 2010 I noticed erratic boost pressure readings sometimes the boost pressure would read zero under partial throttle where it should have been reading12 or 14 lbs boost. Replaced MAP sensor and the boost reading problem went away. April 1 2010 took the truck to Cummins Northwest to purchase a new IAT sensor suspecting the stalling problem could be due to a faulty IAT and the cold outside air. While there a mechanic looked at the truck and noticed the sticker saying the last ECM program re-flash was in 1999. He thought a re-flash with the latest program might help the problem and I agreed. He re-flashed the ECM and kept his scan tool hooked up shut off the truck and restarted several times and noticed the IAT temp reading sometimes went to and stayed at 160. When it went to 160 the truck would not re-start until enough cold air came through to cool the IAT to below a 130 reading. I went home, changed out the IAT with the new one from Cummins, and took it for a test drive. Still have the stalling and hard starts but not as bad and the idle rpm hunting seems to have gone away. Yes, I have checked the grounds on the ECM and PCM. I have also cleaned all battery connections and used dielectric grease everywhere. So I'm Kind of out of ideas here. Today I'm going to get it up to operating temp then shoot the exhaust temps of each port on the manifold looking for enough variation to indicate a plugged injector or one that may have a lower pop off pressure. If I can't find anything there I may pull the connector tubes part way out and rotate them so the O rings seat in different positions and see if that does any good. I'm open to any and all suggestions to solve these problems. Thanks Jim