Hmmm. OK, I think what I have to do no matter what is get my hands on my friend's telescope so that I can get a really good alignment set, and try other solutions in conjunction from there too. Thanks for this!
Actually, you may be better off just skipping over the alignment steps when they come up on the controller. For the long time periods you are using you will never get a good enough alignment to keep the readings correct.
So you just set up with a manual alignment of the mount then switch on the controller. When it asks "Begin Alignment 1) YES 2) NO" press "2".
The mount will assume it is perfectly aligned so the readings wont change as it rotates.