Why are the values negative in the Arap bin and much higher in the stock 89 bin?
Arap on left stock 89 on right

 

There can be a hundred different other things going on else where in the chip.

To understand some differences between .bin files, means looking at every entry, and seeing how that effects what your trying to understand. Timing is rather easy, fuel gets more complicated, to understand, least for me.

 

I understand that I have to look at a bin globally. But in the ARAP bin its actually taking away fuel vs. the stock adding. There is also a lot more timing in the ARAP bin. That leads to leaner burns, no?

Would it be safe to assume that I can add some fuel to the ARAP bin? or atleast not take away any? I have a flat spot between 4000-4500 rpm that I am attributing to knock retard and possibly lean fuel map.

 

Just as one example,
if the PE AFR vs CT is in the range of 12.0, in the ARAP, and the stock 13.0, then it would in fact still be richer, even thou the trim is a lean correction.

Without a WB, you always tune to a rich condition first. ie experiment by adding fuel. Since going lean can be very damaging very quickly.

Again, just using the info you've supplied.
Car is flat at 4-4.5K.
First try adding a little fuel, say 3%.
Note results.
If the condition is worse, the try removing 2% fuel.
Then try subtracting a few degrees of timing.
Note results.
If worse try adding a couple degrees.
The try the best timing with the original fueling.

All the while double checking the plugs to see what's really going on. You can't fully/ completely, count on the K/S and O2 voltage as indicators of what's going on.