2005 F-150 Lariat SCREW 4x4 54.4 3V 170,000 miles

Nearly every time it is started cold, it will misfire until warmed up. Usually just P0304, but will occasionally throw an additional P0308.
Currently has a persistent P1000 and B2477 (I had these before and they cleared but are back again)
At one point, had a runner control stuck open (can't remember the actual code)
O2 Sensors appear to be switching properly when warmed with no misfire present.
Fuel pressure (ready by OBD) 39 psi.
@ Idle Fuel trims: LTFTB1~+14, LTFTB2~+12
@ 1000rpm Fuel trims: LTFTB!~+4, LTFTB2~+22
STFT usually bounces around -3 to +7
I removed O2 sensors and ran it only to have misfire still (was looking at possible clogged cats). I wish I had of swapped the sensors from side to side to see if P0308 became more common.
Here is everything I have done to it. The first 5 items I did initially since I had just bought it- I hoped they were just old and worn.

-New Plugs
-New COPs
-New Injectors
-New Fuel Filter
-New MAF

-New Throttle body (mine failed while running diagnostics)
-New runner control module
-New Intake Manifold (decided since I was taking it off, may as well replace - the gaskets did look suspect)
-Top engine cleaner
-Smoke test (passed)
-Replace 1 VTC solenoid (had appropriate code when it failed)

I am convinced I have either thoroughly tested (an replaced) everything under the hood that it could possibly be.

I have begun to wonder of my PCM is failing since P1000 and B2477 came twice (this time seems to be be sticking around) OH, I also had a PATS code when P1000 came back, but it cleared.

As of right now, I think I have only sunk about $500 into it - each thing I did, did make it just a little better (gaining power and better MPG), but the misfire always remains.