backfiring through air filter

Sounds like it is a really bad misfire. Since you have replaced the Ignition parts, i.e the cap, rotor, plugs and wires, you better check your Ignition Coil, it could be old and arcing out the side which would cause a nasty misfire.

If this wasn't happening before you tuned this engine you might have 2 ignition wires crossed check the firing order