Wife had the clutch replaced on her Compass at the Jeep dealer 3 years ago for $1200. The Compass is a bitch to replace the clutch due to the traverse mounted drive train.
Stop going to them for such work, RARELY does a flywheel need to be replaced. My flywheel still looked like new at 192k miles when I removed it to convert to an automatic transmission.
Whoever is quoting you $3750 to replace a clutch, who now says the flywheel needs to be replace too without even having seen it yet, should be strung up and hung by their balls for daring to try to rip people off like that.
Replacing a clutch is a relatively easy job that can be done in 3-4 hours... or less if you do such work regularly.
By the way you can buy a good quality clutch kit for a JK for >$500. Even a Mopar clutch kit is only $450 at Summit Racing. That plus, say 5 hours of labor at $200 per hour to be generous, = $1500 is a price I'd consider fair for a shop to charge.