So, I am new to the forums so I'll start this off by giving you details on the bike and explaining what I have done up to this point.

2012 XL1200N
V&H Shor Shots Staggered Exhaust
Stock Intake
V&H FP3
1" Tank Lift
Wire Tuck
Coil relocated between V with equidistant plug wires
NGK Iridium Plugs

The Problem:
Running out to cabbage patch fro bike week back in March the bike started losing power and threw codes P1352 and P1354 (codes pointing to front cylinder coil)
I limped the bike home on just the rear cylinder, and because the codes pointed to the coil I ordered a new one.
New coil arrives, I ohm out both coils and they both give very similar results but I go ahead and throw the new coil on (I have not tried to start the bike again at this point). Fire it up and it runs great until it warms up and then back to firing on just the rear cylinder again.
I let the bike cool and swapped back to the stock coil out of curiosity, fire it up and it runs great until it warms up and then back to banging on rear cylinder only.
Work gets needy and I dont have time to revisit for a while.
Fast forward to a few weeks ago
Finally get time to work on it again so I start checking connections and wires, swapped the plugs so the plug from the rear is in the front and front plug is in the rear, no dice same result. Compression on both cylinders was very close so I don't think that was the issue.
Pulled the injectors and hooked them to a tester, they cycle like they should and I go ahead and clean them out on the test rig and reinstall everything, still doing the same thing.
I notice when I pull up sensor data on the bike while its running on one cylinder that it is showing an engine temp of 388 degrees, mind you at this point the bike has only been running for about 10 minutes, check with IR Thermometer and get about 230*F not 388.
Swap out ETS for good measure, have intake off, run bike around block several times, runs great. reassemble everything.
Run to gas station a couple miles away, fill up, return home. No problems.
Go to take bike on a night ride the same night and let it idle about 10 minutes while talking to someone, jump on bike and prepare to take off and BAM front cylinder shuts off on me temp at that time 314*F.
Start bike this morning, runs on both cylinders for about 2 minutes and then drops down to one again, temp reading 230 at the time of the cylinder drop.

Any ideas on what else to check?
Im at a loss and really hoping it isn't an issue with the ECM and don't want to tow it to Harley until I have exhausted all possibilities other than the ECM.