Engine misfire - clutch vibration - some what rough idle?

[blueapple]

What do you guys think?
I've heard that one of the reasons for the clutch to seem "vibrating" which then transmits through the clutch pedal, can be caused by engine misfiring.

Here's what my clutch is doing: well, it's very werid, one day is better than another, say, if I start the car cold and drive it, the clutch first seems to be operating just fine, smooth mostly, not any noticable vibration. I go 40-50 miles, about the same, then I come to a stop and go traffic, a few strokes later, the pedal feels notchy, vibration can be felt at the tip of the pedal, right before pressure build up, and it seems to be some what sticking on the up stroke.
This happened after I changed out the old clutch, so, initially, I was looking for mechanical failure. But then the mechanic who did the job said, my car could be possibly misfiring.

Which makes a little bit sense, especially in an engine like 5sfe, everything depends on a perfect balance, and if one of the cylinder doesn't fire once in a while, it might cause what seems to be a vibration. ( my clutch vibration seems uniform by the way ). But why my ECM doesn't detect a problem? Not enough emission mess-up to triger the O2 sensor?

Another thing I've noticed lately is that, when I shift around 3 -4 k RPM, and lift my foot around 2-3K rpm to engage the next gear, the vibration almost disappears. BUT, if I shift around 2-3k and engage around 1.5k or so, ( like 4-5th gear shift ) The vibration is much more noticable.

I understand that the fuel return is usually around 1.5k to 2k. So, when I let go the gas around 4k rpm, the fuel will momentarily cut off and return around 1.5k rpm, so the engine is basically running "empty" , or firing without fuel between that range. Which kind of explain the misfiring causing vibration theory. Also, when the AC turns on, the vibration seems to get worse.

So, I'm confused, my wires are around 9K ohm each. not high at all. All plugs are new. A clogged fuel filter? but that shouldn't cause just one of the cylinders to misfire, right?

Car is 100k 96 Camry, good power and smooth ride. with stock wires and most likely stock cap and rotor. Car has slightly higher HC reading than average, but still very much within spec, high NOx, but passed emission just fine.

Car also idles a littel rough, it's got that typical camry vibration at idle, but also seem to surge a little bit once in a while ( very lightly, and no, it's not the front radiator fans kicking in, I know how that one feels like ).

Anyone with any opinions?