How to fix clutch on 1998 Honda civic DX?

I noticed this problem about 3 days ago . When I shift gears its seems to hesitate before shifting in all gears 1st-5th, except reverse. I have been driving in commute traffic for about a year now, about 50 miles per day. Made 2 road trips over 600 miles up past Yosemite Calif. when going up I had to stay in 1st and 2nd for quite a while. I've got 140,000 miles on my car now. It also is making some sort of knocking or taping noise that sounds like it's coming from the rear right, happens when I'm slowing down, in sync with tire rotation. That has been going on for 5 months. I had new brakes front and rear put on and wheel bearing hubs. Does this sound like clutch problems?