You're getting bent over on the flywheel.
Sachs clutch kit is $300 (
link), flywheel adds $400-$500 parts cost and takes an extra 10 minutes to do once you're in there, so the added $1100 is absurd. $600-$700 labor for an extra 10 minutes?
BTW, when I did my clutch at 96k, the flywheel was fine. Maybe buy one yourself and have it on hand. Ask to see the flywheel when they get the trans out and decide for yourself. You can always sell the new flywheel for little to no loss if it's not needed.