Well, the shop has the car back together again, but there are some minor issues.
(1) The clutch engages fine, but real close to the floor. Apparently a spacing issue between the throwout bearing and the clutch pressure plate fingers. Which means the drivetrain has to come out again.
(2) The button underneath the clutch pedal to enable the engine starting is not being engaged.
(3) Shifting into some gears isn't working right, perhaps something got knocked out of alignment in the shifting linkage.
Doesn't sound like anything that isn't fixable, though.