I switch between coconut husk fiber and paper towels. I used newspaper once but I usually run out fast because I use it with my conure. I guess the easiest thing to use to monitor bacteria growth would be paper towels because its easier to spot feces and urine. You clean it when its dirty and disinfect the enclosure and that's it!
If aspen bedding caused RI's I don't think any snake keeper would use it! Is there a different vet in your area? Yours sounds very unreliable. :/