Mmmm I dont think the ecu has anything to really do with elevation change, especially since that is one of the bennifits of FI. Plus you've been driving for a few months now with no issues. That being said. I'd check oxygen sensor, timing, and for a leaking/stuck Fuel injector. Also you mentioned the engine was rebuilt. Just to be sure everything was done with correct specs I'd check compression just to be sure. Give us and update.