Thanks for all the replies guys, I have been very busy the past few days, but I am going to rip out the AOS tomorrow after work to see if it helps any. It didn't show any signs of leaking though when checking the system. I am also looking into other shops on Long Island that I can bring the car to for one last hope of finding out what the issue is. Moto East, you guys are almost 4 hours from me as you are located in PA and I'm in NY so I don't know if that is possible for me to drive the car as is that far of a distance.
Here are some logs I promised - the first one is with the Delicious Tuning 'hybrid' map & was a terrible drive, and the last two are with Full Blown's basemap installed. The "highway cruising" one probably shows it the best, although it gets much worse.
FBM Highway Cruising Hesitation
FBM 1st-2nd-3rd Driving
DT Hybrid 2nd-3rd Gear Driving