Chasing a Ghost. Timing at idle.

[08lmm72mm]

Hey guys, I've been slowly fixing every issue on my truck trying to make it run like it used to. The problem I'm having is a persistent rough idle and sluggish throttle response with more than usual black smoke until the turbo lights. Even sometimes on my bigger tunes I get the odd pop or light backfire at 16-1800rpm getting heavy on the throttle.

Things I've changed:
FPR new bosch unit
New Harmonic balancer
Harmonic balancer dowel pin (bent)
Oil pump drive gear dowel pin (was bent)
Rebuilt Fuel filter head
Installed 1/2" CP3 inlet fitting
New 1/2" fuel hose to and from the fuel filter housing
Changed MAF
New MAP
Clean new dry filter

I've testing the CP3 with a tech 2 commanded rail pressure at the way up to 180mpa without issue. Can cycle the vanes in the turbo from 0 - 100% without issue. Installed fuel pressure gauge in bleeder screw on fuel filter housing confirmed 8psi from lift pump.

Balanced rates are:
Cyl1 0.9
Cyl2 -2.5
Cyl3 0.8
Cyl4 0.3
Cyl5 -0.3
Cyl6 -1.8
Cyl7 2.3
Cyl8 0.2

Calculated fuel rate bounces from 6-10mm3.

I'm at a total loss. Injectors have 100,000miles on them so does the turbo.
Main injection timing is 2 degrees at idle.
Possible my ecm is acting up? Zero boost leaks.
Going to check injector return rates next.

Any help is appreciated

 

[08lmm72mm]

There is no codes other than a once and awhile p003a. Also #6 injector when it was quite warm out the other day was reading up to -3.8

 

[08lmm72mm]

I have a log here if someone wouldn't mind taking a look at and see if anything sticks out. I'm curious why my maf looks like it dips around frame 300 at WOT.