I'm not new to solving problems with the SOHC neon, I have had a 95 SOHC one since 2002. I have experienced all sorts of issues but this one has me baffled. First, let me tell you my current build before I describe the problem.

95' SOHC (112,000 miles)

Cold Air Intake
Pacesetter Mid-length Headers
Straight Pipe w/o Cat
EGR removed
Purge Canister removed
Granatelli 2-3 ohm Plug Wires (replaced 3,000 miles ago)
NGK Iridium Plugs (replaced 3,000 miles ago)
OBX Underdrive Pulley
Adjustable Cam Gear (Set 2 degrees advanced for better lower rpm power)
Gates Timing Belt Set (replaced 10,000 miles ago)
MPX 60mm Throttle Body
Mopar Racing ECM for 95 SOHC MTX
Walboro 255 lph fuel pump (replaced 30,000 miles ago)
All new seals and gaskets (replaced 10,000 miles ago including front and rear seals and head gasket)
New oil pump (replaced 10,000 miles ago)

Now, the issue.

I was cruising at hwy speeds (70 mph) and suddenly the engine suddenly boggs down like it suddenly lost a cylinder or two. Only lasted for a second or two before coming back to normal. Happened about 4-5 times during my 30 minute drive home from work. Next day, everything is fine. Again, on my way home it happens again, but this time it doesn't go away. Luckily it happened within pushing range of my house (which sitis at the bottom of a 2 mile long hill. I get it home and it starts back up like nothing was wrong. I decide to drive it around to make it mess up again to diagnose it. I get it to start messing up again and this time it starts to act weird. It will barely idle, then it would catch and rev up to about 2500 rpm on its own and die back down to barely idle. It would do this off and on along with a few backfires on it's way back down to barely idle. I pull plug wires 1 and 4 with no effect on the way the engine runs. If I pull plug 2 or 3, the engine dies. So I believe it is the coil pack. I change the coil pack. Everything working fine. I drive it around for about 30 minutes without as much as a skip in the engine. I thought the problem was solved. I take my daughter up to her school for her art show the next day. On the way home, it happens again. A lot worse. Barely idle and backfires like crazy. I don't quite make it home. After 15 minutes of sitting on the side of the road, it starts right up like nothing was wrong and I get it home. I pull in the driveway, shut the engine off and immediately try and start it. It won't start back up. This engine has not overheated during any of this.

Next morning, it starts up like nothing was wrong, so I pull it into my garage and start checking everything.

Timing - Nice and tight. Hydraulic tensioner working properly. Still lined up. Adjustable gear still nice and tight so it's not slipping while I'm driving.
Alternator - Charging normal. 14.3VDC at idle.
Spark Plugs - Clean and dry
Plug wires - still at 2-3 ohms
Coil Pack - Brand new and firing all 4 cylinders
Thermostat - Operates properly. Opens at 190 degrees (tested by putting in a pot of water on the stove with a thermometer and watching at what temp it opens at)
Fan - Operates normally - Turns on with A/C and also when engine reaches operating temp.
Temp Sensor - Operates normally
Wiring harness - no breaks or worn/dry rotted areas
DTC - Multiple cylinder missfire is the only code (find this odd since i have no Cat or EGR or Purge Solenoid which it should be throwing a code for)

My next thought is to change out the cam sensor or put the stock ECM back on. That's all I can think it could be. Is there a possibility that the cam itself could be pulling away from the cam sensor when the engine heats up and parts expand? Could I have some valve springs failing? The engine backfire is telling me that at least one intake valve is open when the spark plug is firing.