I like rainwater because it is soft, not many minerals, and slightly acidic, so it makes a nice flush that you can run a couple hours, or weeks and drain the sediment out. Your well water is probably fine if it's not terribly hard. Where you get into trouble is adding a gallon every couple of days because something is leaking, that will plug a radiator up with hard water deposits. One time flushing won't really matter in the scheme of things.
I'd use conventional because you might change it annually, because you won't get the hours to change it more often. It will be dirty, but the oil will not be broken down, where a synthetic would last longer. If you're going 24/7 and oil changes are downtime, then synthetic allows a longer change interval, and save money. Year old synthetic with the same dirt isn't going to protect the engine any better than year old conventional, they'll both be dumped just because they're a year old.
The dealer might have some parts and glass, the wiper and possibly latches will be cheaper if you can match the names and numbers off them and order outside the dealer. The glass can come from a glass shop, don't know which would be cheaper.
Your tank might be fine if you keep up with it. The plastic tank is a last resort if problems come up, or you really want to keep fuel fresh.