See that little metal fork looking think on the big output gear, that is what is telling your actuator its position. As it slides across the circuit board I bet the resistance changes. Get the grease off of the area that it contacts, maybe even clean it off with some contact cleaner and try again.

Are you pulling the RDO fuses ?

I believe there are 2 RDO fuses and a HVAC fuse. My 2 RDO fuses were on the bottom corners of the fuse block, the very front fuse and the very rear fuse, bottom row.

 

I'm still questioning if your climate control unit itself has issues, seems I've heard of some people having to replace those. If your actuator can move full travel in both directions AND the resistance is linear (not jumping from 5 to 0 etc...) I'm thinking it may be ok.

I also don't think your actuator can "loose timing" with its new design.