that does seem pretty high and I would have knocked off some of the labor if you assisted me and I actually did need you and use you. But, anyway.
Wow, using silicon sealant to seat a non seatable connection is really not professional at all. This should have been stopped. House movement and the likes will cause this union to leak very quickly. This should be re opened up and fixed properly.
The upstairs shower leaking. Are you sure its the drain and the connection? How do you know it might not be the pan or the grouting or whatever is leaking? many showers leak and its not the drain or plumbing. Many times its a compromised pan and or grouting or caulking in corners. The most leaked area in any shower is the corners directly in the direction of the pressure of the water exiting the nozzle. Or the ones behind you as you face the shower nozzle. Now if you have a contained unit, this does not pertain, of course.
Do your inspection of corners and joints and re caulk if needed then do a leak test.
Wow, plumbing problems are just as frustrating as mystery electrical problems.