Losing three degrees is not going to make or break a beer, though it is strange that you did in a cooler. It makes me think something is off in your process that you aren't mentioning here.
I can't imagine any problems you would have from not draining the be completely, though I guess it could offset your efficiency slightly if there was a lot of saturated wort already in the tun when you started sparging. The main problem from letting your mash drop low is that some people find their systems more vulnerable to getting stuck if it gets cool.
I expect there to have been more fermentable sugars extracted than was intended, but since I mashed at about 158F for an hour before the trouble started, wouldn't those less fermentable sugars also be in solution?
I don't understand this reasoning behind this sentence. You can't have relatively more more-fermentable sugars and relatively more less-fermentable sugars at the same time. One turns into the other, so if you are getting more of one you are getting less of the other.
I doubt the extra time impacted your efficiency much, and the temperature drop is not terribly significant. Your first 15-20 minutes are the most important in a mash, so if you hit 155F very quickly then that would have a more dramatic effect than if you gradually drifted down over the course of an hour.
The extra time very well might have caused some simplification of your sugar profile, which will give you a more fermentable wort, though it is hard to say how much.
A HLT and a mashout are all well and good, but it sounds to me you just need to figure out why you are getting a stuck mash.