I'm would have also said incorrect gear ratio. I see the post about high trans temps after gear ratio chance pop up ever 6 months or so on the forum. Other than that, did you flush both aftermarket cooler and cooler in the radiator before installation? Depending on what type of trans failure you had earlier there could be a ton of junk that was put through those coolers.
Edit: About the surging I had a similar issue after I installed my trans but after about 100 miles the pcm had enough time to go through the re-learning process and went away. I emailed Dave about it and said that if it wasn't gone in 2 day of stop and go driving to give him a call....went away before 2 days.
