Your problem with the flame color and pattern sounds just like the problem I had with our propane patio heater after a spider decided the tubing to the burner looked like a cozy cave for its nest. It took me a long time to get it clean enough to burn normally. I had to take the whole thing apart to do it too.
The flame burned very yellow and the flame front was kind of "lazy" looking, with long flame "fingers". Very sooty burning too.
I'm crossing my fingers that the water heater, furnace and refrigerator in my HiLo doesn't ever look inviting to our 8-legged friends. And, I have no clue how I could ever "spider-proof" those areas.
- Jack