I think I might have a serious problem.

I had my car in the shop a few weeks ago to get new motor mounts, both front driveshafts, and a bunch of other stuff. Within the last week, my car has been making an awful put-put sound and the transmission is shifting hard in 1st and 2nd gear. I pulled the plugs to see if any of them are going bad, and I found that cylinder 3, 4, and 5 are filling up with oil. Does that mean it needs new piston rings, or does the entire motor need to be replaced? I also noticed that when the car shifts into 2nd, there's a clicking noise from the front left driveshaft. Does that mean something has come loose from the new ones I just got put on? By the way, my car is a '96 Acura 2.5 TL.