So to clarify, you took the plugs and wires apart but didn't replace anything..and the misfire is better but not gone? It still sounds like you'd benefit from some plugs and wires to me. Get good quality wires and some NGK plugs. Also, I don't know about that particular setup but usually the COP setups still need a boot between the coil and plug, don't assume that just because there's no wire there, there's no failure point...they're supposed to be replaced with the spark plug wires. Rock Auto shows an AC Delco plug wire set for $25, the boots are a lot more so I'd look around on some forums to see if there's a cheaper place to get them (straight from Toyota?), and obviously plugs are cheap.
This doesn't sound like plugged fuel filter because that would tend to get worse with higher flow rates (in other words, as you revved it higher under load it would hesitate worse). Of course, if you've never done the filter that wouldn't hurt either.
Bryce
