recently tuned up my newly bought 94 sr5, ran into a problem...
cap, rotor, plugs and wires replaced. it had 111k when i did the tune-up, and i think the plugs were the original, the electrode was worn down to where the gap was probably 1.5 mm, however it ran fine, just short on power. i used oem everything, with ngk plugs. gapped @ .08mm, the factory gap. ran with much more power, but felt like it was misfiring every 30 seconds or so. pulled the plugs out and gapped at.095mm as recommended by a buddy with a tacoma, and it runs better, but it randomly get sluggish for a few seconds, then comes back. im at my wits end. please help

Many people recommend not altering the gap on the factory plugs. Just as a test, you can temporarily try a cheap set of gapped plugs and see if this corrects your problem. Check the resistance on the plug wires. Another possibility is the computer is just taking a while to get used to the new ignition system and it will solve itself in a week or so.

Changing the fuel filter may help, its underneath about mid ways on the passenger side.