Well, I've measured and an aftermarket cooler would put the fans literally touching the back of the lower card.
What if I got one of these:
Hopefully I can move the top card higher (I don't have space to move the bottom lower because the psu is mounted in the bottom). Would the extra slot space make a big difference?
Or what if I put a sheet of acrylic (like you'd use for a case window) between the two cards? Or is this more likely to start a small fire?