Doh! After I posted this, I just happened to think about this while sitting at a red light. Why not just cool the sample to the post boil/cooled temp. I'm writing down everything just to try and get a handle on the whole process. I sampled gravities from each running, just to see how much sugar I was getting out of the mash and subsequent sparges. At this stage, I'd rather have too much info than not enough, then sort it out later in front of the tube with a cold one.
"If you don't try it this year, you'll just be another year older when you do" - Warren Miller
WARNING: Drinking may cause memory loss, or worse, memory loss.