Does it do it when you lift the throttle? If so then the most likely cause is and air leak in you exhaust manifold, or it's running lean (or possibly rich) on the overrun.
Mine backfires on the overrun, but due to the exhaust system it sounds more like it's farting

Actually I've notice a lot of 3S-GTE's do the same when you do the filter and exhaust mods, my MR2 is the same, though I can really make it backfire by playing around with the settings on the Motec, even got flames out the exhaust once
Plug gap should be 0.8mm (0.7mm for 16PSI+)
I have a Blitz pod filter on mine, but I'm going to change it back to standard as I haven't got time to make a cold air box and I don't like it's filtration. Other than better intake/BOV sound theres' not much extra performance to be gained from a pod filter on an otherwise stock engine.