My 2001 Honda Civic stopped running?

I was having trouble getting up hills and past 20 mph and then on the highway it stopped accelerating. I also was having trouble getting it into 2nd gear, it would grind hard.

So I got it towed to the shop and they can't even inspect it because it won't drive at all. They want me to pay for a new clutch, but I have to wonder if I'll be paying for a new transmission or engine next. Can anyone help me out here?

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