What kind of screws attach the capts chairs to the floor on an 06 heat? I want to pull mine to give everything a good cleaning, just wood screws or is there a toggle bolt or something I need to look for?

if it's the same as the 05, most are just wood screws, but 1 possible 2 are thru bolts which you can access from the ski locker in the floor.

Did the wood survive the removal/reinstallation on yours or did it get wallowed out?

My 06 Heat has a fiberglass floor. Seats are screwed down with wood screws.

It survived.