I have a 1995 SSEi and it chugs (shakes/hesitates) when accelerating past 40(-ish) mph. Started about a couple of days after I replaced my alternator (refurb). It'* not a continuous shaking. Shakes only whenever I press on the gas pedal and accelerates.

It also has a problem with accelerating from stop, like its hesitating to accelerate from stop. It goes, but its slow and you can hear a noise like the engine is getting overworked I guess. I'm thinking it might be connected to the previous problem.

Anyone know what might be wrong?

Things I've done that I thought might be the problem:
-Replaced the fuel filter
-Replaced the PCV valve
-Checked air filter (looks clean so I didn't replace it)

Had that on my car. Started and ran fine. Sputtered and hesitated when I leaned on it a little, such as accelerating on an entrance ramp. Turned out to be a cracked ceramic insulator on the #4 spark plug. It would only arc under load.

Check your plugs and wires.

Replaced the spark plugs and wires. Looks like its stable now. Don't know why I didn't think of that earlier. Thanks!