The knock sensors don't even touch the timing in the first two gears..?
actually it did ADD 4 degree's of timing in I belive 1st gear.
That may be one of the problems you are working against.
The tuner put a positive value in the knock sensor retard scalar.
This isn't wrong, many people do it.. but.. in your case..either too much available spark or not enough fuel is not making the car happy.
If you had the PRP, y ou could remove that positive value from the KS adder then "sneak up" on a "max spark value".
hope this helps....