I also installed the toilet mounting bolts to the flange using nuts to hold them in place. There is plenty of
room for the nuts in the ample recess under the toilet. Any problem using nuts on the bolts to hole them in place?
This is actually exactly what the better plumbers who install a lot of toilets do. Terry does it, and recommends that we do it. He double-nuts the tank-to-bowl hardware as well: one nut and metal washer holding the bolt to the tank, then the second rubber washer, second metal washer, and nut (in that order) under the bowl holding the bolt to the bowl.
How tight should this supply line nut be?
Hand-tight plus a quarter-to-a-half turn with pliers is about right, unless you have very strong hands. Sounds like it's fine.
The original supply lines were all made with solid tubing.
Is there any advantage to removing the solid supply tube and replacing them with new flexible supply lines?
Most folks use the flexible lines these days and hard lines aren't generally required by code in almost all jurisdictions. NYC still, I think, requires hard lines by code, although lots of folks (including the maint staff in my building) ignore this. If the old supply lines still fit readily (i.e. you put the toilet back in basically exactly the same spot, tilted and lined up exactly the same way), then it should be fine. However, one reason that you may have had an issue reattaching the supply to the tank without leaks may well be the slightly-different angle that the hard line is going into the attachment to the tank. Most likely, a braided hose would eliminate the need to tighten so hard. Don't use the "flood stop" ones; they are renowned on here to cause problems. Bottom line: new braided hoses, looped around from the outlet to the tank, are like chicken soup: can't hurt. Terry replaces the hoses when he installs a new toilet (and usually the stop as well, but he does a complete job for the money he is paid).
Thanks again for all the great and helpful information!
Our pleasure. We enjoy helping/educating folks like yourself. You really took the knowledge and put it to good use!