Sorry for the delay. Finally got some time today to run some testing. A couple things regarding the tune you attached (2012_EB2.3_LTH_91-93_basefile)...
1) I assume the intake cam phasing limit table should have -65 degrees, NOT +65 degrees in there?
2) I see you left [ECM] 44351 - MAP Max Delta above BP vs. RPM zeroed out. Should this have a boost curve in it (in inches of Hg?), or is all zeros still OK for a boosted car?
3) Max Aircharge Load is 1.00. Should it be higher, like 1.90?
4) I see that you have Pressure Density Scale "disabled." Why, and what does that do? I haven't seen anyone else change that.
5) Regardless, here is a log with that tune (aside from changing #1 as I assumed it was a type-o):
Attachment 105684
In the mean time, I did a little more tweaking using a mashup of things from the Edelbrock tune and Coyote Cookbook, etc. It runs pretty well, save for a few things
1) Here is that tune file:
Attachment 105686
2) Here is the log file:
Attachment 105685
3) I still seem to be having an overshoot on tip-in/undershoot on tip-out situation which also directly corresponds to some very large torque errors.
Attachment 105687Attachment 105688
We're making progress, but the root of the problem still seems to exist.