I would expect the shooter lane, arc, and apron all to have been waxed in the past. I have not used naphtha as a wax remover prior to clearing (or painting). Not to say it won't work....I don't know. I use a product from the automotive paint supply called "Wax and Grease Remover" prior to painting. Even then, there have been a few times I got "fish eyes" and had to repeat the prep process and respray with successful results. Wax and silicones can be a b**ch to completely remove. Probably you had good results on your inserts because they are plastic (and easily cleaned) and the wax didn't seep into the pores like it would on wood.
You don't need to sand to 1000 grit. Better to stop at 400. I have had good results stopping at 320, especially if I am using rattle can paints. The 320 or 400 will leave more surface area for the applied paint to adhere to.
Spraying the sanded dust off with compressed air may actually be hurting you depending upon the compressed air source. Is it an oilless compressor? Has anyone ever put an oiler in the line to lubricate air tools? Has the air tank been drained of water? Do you use a coalescing filter to trap water and oil? You just want to avoid the possibility of spraying even the minutest (is that a word?) amount of oil or water onto your surface prior to painting.
Finally, mixing products (oil based, lacquer based, polyurethanes, etc) can be tricky. If you are using Krylon products, call the 800 number on the can and ask for Tech Support. They should be able to offer specific troubleshooting advice. In general, oil based products can take a long time to dry, and if you apply over a surface that has been previously coated, and not COMPLETELY dry, then you will get a defective finish. You will note on some manufacturers instructions to apply additional coats within an hour, or after 48 hours. I have found that 48 hours is not always enough time. I have waited as log as one week to apply additional coats to avoid problems.
Finally, I don't have any recommendations for a clear rattle can product. I use rattle can colors, but for clears I use automotive two part mix.