Semi rough idle and shutter under initial throttle

[poneypower]

I've been trying to figure this out for months and am at my wits end. the car is a 2000 Focus SE Wagon. It has 101k on it right now. Here is what happens. Just above idle (wish I knew the RPM) the car vibrates quite a bit. The idle actually sounds fine, but there is a vibration that can be felt throughout the car. When you depress the throttle it gets worse for just a second and then once it has throttle it's fine if you keep your foot on the gas just a little. If you turn on the lights or hit the window button it gets worse. the other thing is I think the bearings in the alt are squealing.

While it's driving it's fine. Only happens when sitting and on initial acceleration. Here's what's been done so far:

Plugs (me), wires and coil pack (previous owner), the rest are all me, new PCV valve, new IAC, cleaned TB, cleaned MAF, replaced cracked air box w/ new filter, new battery, checked for vacuum leaks, tranny flush (cooler as well) w/ new filter, new TPS. I've checked the motor mounts and they are fine.

Originally the car was rough right at idle. When I changed the PCV the shutter/roughness moved up the RPMs.

I want to change out the alternator or at least get it tested but I don't know if it will help. could this be a problem with the wiring from the alt to the battery and/or the grounds? What about a transmission problem? I do occasionally get a hang in acceleration, which is why I changed out the TPS. It's very rare though and I drive the car a lot every day for work. Any ideas would be appreciated. Thanks

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