Recently, I feel that the car is shaking lightly when I'm driving it.
The car used to be very smooth(very very smooth). But after I had been driving it misfiring, and replaced the spark plug wire, the
car does not misfire again. Instead, like I said, I feel a little shaky (especially when low
RPM). Please help me find out what's happening to the car. Is it because of the clutch? or what?

 

It could be the ignition coil that's going bad. I don't think worn out clutch would make the car shaky. However when you up shift quickly and your tach needle doesn't go down right away, you know the clutch is slipping. To start the diagnostic, do a compression test to get an idea of what's going on.

 

What else could it be? It's been a while now, and it stays the same. I also
noticed that the engine temp is relatively low, I can say that because
even I drive it hard and the outside temp is crazily high (like 94 degree),
the engine temp stays less middle position.(I don't have pic to show)

Assume the gauge is fine, can anyone thinks of a reason? And the shaking?

 

Inspect your motor mounts for cracks or any that are broken.