Ya now that I know that the green wire doesn't go through the link I conceded that it is not that issue.
As far as spark I have added almost 12* down low (where it was only about 4*) from what I had on motor because I believed that it may not have enough. The issue still persisted.
Burst Knock is still enabled.
As for being afr, it may be very fat. As it has a .028 nitrous and .014 fuel pulling off rail in the direct port. As you can see the lambda is as low as .69 in first in the run.

 

It wouldn't hurt to log burst knock as well because it looks like some timing is pulled.

 

Ok. Well now I'm back to not being convinced its not something to do with the x link. This is a log pulling off the APP sensor 1 prior to the tac. The truck sprayed but the throttle itself never opened to 100%. I also could also tell it never went above 50% due to the short shifted first and MAP.

 

Log file:

 

Don't see what the commanded TP was. If actual TP and commanded TP do not match REP mode will be triggered, a code(s) will be set and the throttle will be disabled. Log ETC Desired Position % and ETC Position %.