That's robbery. Find another mechanic. It's been a bit but I THINK it was around 800 in labor and there were a few other things done at the same time. It's not a hard job.
IIRC... it was a couple hundred in parts. If you're taking it somewhere, labor varies quite a bit from shop to shop so no telling there. It's labor intensive so labor will be higher than parts cost.
Just had a shop replaced my pressure plate disc pilot bearing throwout bearing supposedly machine the flywheel I was charged for it the problem I'm having is it seems to be chattering especially in reverse if I give it enough gas it seems to be somewhat smooth now is that just an issue because it's brand new and I should wait a few months
Clutch break-in typically takes a few hundred miles but I'd make the shop that did the work aware and see what they say. Could be several things but I'd give it a bit and see if it cleans up before pulling it back apart.
According to the manual & many reputable threads ive read you are not suppose to resurface those flywheels, they have a dome like shape to them & it takes special tooling or lathe to do that & its highly unlikely that most machine shops are set up to do that it also states unless theres visible damage or heat spots you just clean it up with 180grit emory & call it a day!