You are unlucky. Once in a while a motor doesn't like being transplanted and there'* really no rhyme or reason behind it. The majority of the time these motors take a transplant w/o problems.
The SC, Dex and programming etc should have nothing to do with it. And you aren't swapping anything like knock sensors etc, so nothing critical is involved.
Try and look at the bright side. You will be able to do it in half the time and all the bolts will come loose w/o a fight. At least that'* how I looked at it when it was me.
00 Regal GS: All kinds of cool stuff.