AWGD8 wrote:I realized that they only removed it and never replaced since I was very meticulous measuring what came out out of my transmission when I was flushing it my own. I was about 3.5-4 quarts short when I fill it up with ATF.
If true, it's amazing that your transmission clutches aren't shiny, bare pieces of metal. 3 quarts low can be catastrophic in any automatic transmission as they are quite intolerant of over and under filling.
However, a single quart low may be a stretch to explain the OPs issues. Usually a quart low would not lead to noticeable issues or just issues when the fluid is cold (and more dense).
VSD may be the cause but I think unlikely. Maybe a problem with the transfer case/ATESSA system?