I have completely edited this post as I have found new information since I first wrote it.
First, after tuning the latencies a little more (small changes of .02 per flash), my short term and long term fuel trims have steadied. I am still negative (learning is at -4.xx), but am getting close (keeping injector scale the same).
To help others, if they run into latency whoes (like I did), I currently have 1.40 set at the 14V setting. I am gonna drop this even lower (to 1.36). Once I have the latencies set, I will post them up (I am currently using 65x.xx as the scale, I typed in 660 and it automatically converted it). I originally also modified the MAF table, but after reading for hours, reverted back to stock settings (I am using a shorty intake, but the tube diameter on the MAF housing is identical to the stocker).
Please note I am also using a UTEC. I am, only using enginuity for idle tuning purposes (I don't like the open loop fueling on the UTEC, so I would rather keep it shut off).