2003 Hyundai Elantra Manual Transmission/Clutch

I bought a 2003 Elantra GT with about 80K miles on it in September. It’s the first manual I’ve owned, although I’ve had some prior experience with driving one before. Once I became comfortable with the car, I noticed 2 things: first, the clutch didn’t seem to catch until it felt like it was all the way out, and secondly that when I moved the shifter from first to second, their was a hiccup, like something wasn’t lining up correctly (this only happened in the 1st-2nd transition). Over thanksgiving, I took it to the dealer, who said I needed a new clutch, and that this would fix both problems, and for the low low price of $1200, put one in. Now, the clutch seems to catch slightly earlier, but it doesn’t really feel that much different, and the same hiccup is still in the shifter. I’m wondering what could be wrong, if anything, and whether or not I got taken for the proverbial ride by the mechanic.