Ok so more issues this morning. After I reset the computer I took it for a ride and everything felt great. Trans cooler (Hayden 679) felt cool so I pulled off the line to check flow and it came out full flow so I reconnected it and put the car away till this morning.
Drove to work (~20 miles) and it worked great in the beginning. Trans warmed up about half way there then started acting up. First was slightly hesitant after coming to a full stop, then OD (4th) would free-spin when trying to engage and the R's would go up. I have to let off for a few seconds to get it to engage 4th, then it works and holds fine.
Get to work and check out the temps on the trans by feeling it. Fluid in the trans is luke warm, cooler is ice cold. Pull off the line to the cooler to check flow, now I have no flow to the cooler. Last night it would pump out of there like crazy, now ZERO. Even after reving the motor in park would not cause fluid to pump. Checked trans fluid again and its showing overfilled now, like its not pumping any fluid anywhere and its sitting in the pan.
I will also add that I filled the trans correctly during the install, manually ran through the gears, topped off to the correct level and drove it, rechecked perfect. Two days later when the trans was acting up I checked the fluid and it was over the HOT full line so I pulled a little out via the cooler line and filled it up to the correct spot again. Today it appears like its overfilled again like its not pumping the fluid.
I know I still need the tune, but no fluid flow to the cooler doesnt sound like a tune fix to me.