First off the place that wants you to replace your flywheel and Tremec 3650 with 50K miles on it should be exposed for fraud, that noise diagnosis you gave is Obviously a throwout bearing.
Here's my advice find a reputable Mustang only speed shop in your area, this job will be cake for them. Just replace the throwout bearing, if the input shaft is scored change it out, your clutch should be Fine unless the previous owner rode or abused it, while the clutch is out check the flywheel I HIGHLY doubt there will an any problem there either with the low miles you have. While the
tranny is down on the ground it would be a great time to change the fluid. It'll be like brand new after this.