I tried to make squares to keep the dice in place, for those that get moved around a lot. When you get injured, you take your hero level die (up to 3) and move it to the wounded area, where it is clearly out of gameplay.
I only had 3 trophy mounts for a few reasons - aesthetics, space on the board, and need. I haven't played a game where I've won by getting 4 1-fame monsters. But if I did, the game would be over and I wouldn't have to mount it :)
The fame was the only thing I couldn't track easily - but again, it's only up to 4, so we should be able to count (since besides the trophies, you could have artifacts that you were wielding, etc.)
I ordered a cheap 99-cent mousepad to see what it looks like, how large the squares actually are, etc. If anyone wants to test out one, you can pick one (only 1 per household) at artscow:
$1 custom mousepad with free shipping.
http://www.artscow.com/photo-gifts/mousepad/large-mousepad-160
Coupon code: Z099PLAY2KT6T, Expires on 6-30-2013
Of course I'm not posting this elsewhere, as I want everyone to get theirs through Kickstarter. But it could be fun to try out with your PnP game while you wait....
Another option is you could almost have another playmat (different design) for the center of the table to hold the monster level dice and spells....