Rough idle bad acceleration perfectly fine WOT

[KyleThe...Mechanic]

Hey guys, first post on here and I've got something that stumped me 100%. 

I have a 2005 silverado 1500 flex vin code Z. It Idles rough it has terrible acceleration, wide open throttle it takes off like nothing is wrong. It misses on 7 every time, misses on 2 every other time, every other cylinder misses here and there. No misses when in park and rpms are kept about 2500. CEL flashes most the time when accelerating (except WOT) otherwise the light is on solid. It has 220k on it and I have replaced alot of parts. 

New parts

All 4 02 sensors OEM

Plugs OEM

wires OEM 

Fuel pump OEM 

Throttle body cleaned

3 stage fuel system cleaner BG Brand

Air filter believe it or not OEM again

New transfer case (unrelated issue)

 

I have covers the base of the intake with brake cleaner multiple time, no signs of leaks. I've had the smoke machine hooked up 3 to 5 times and again no signs of leaks. At this point what is the best route to take? Remove intake manifold so it's easier to get to and replace the main grounds behind the heads and replace gasket at the same time? Replace the pcm? Replace throttle body maybe? Any other suggestions or recommendations would be greatly appreciated.  

 

[sefiroxx]

Sounds like cmp/ckp sensors

[KyleThe...Mechanic]

Really? I have looked at the data on my scanner, I have a snap on Apollo D8 and that did look normal. As far as I can tell anyways. I did attempt to do a crank relearn and it wouldn't recognize WOT, so basically it wouldn't allow the relearn procedure to be done. One thing I will admit I havent done I'd check the waveform on the cam and crank sensors. Maybe my fault was not thinking anything of the relearn procedure not being carried thru. 

[KyleThe...Mechanic]

I will also add to this, it has NEVER stalled nor has it ever had a hard start condition. This is the reason for me dismissing the crank relearn issue.