I forgot to add another bit of information that is important. This is
a second floor bathroom. That's pretty much the basis of my
assumptions. I'm assuming (another one!) that there would be one set
of lines run to the second floor bath and then split rather than two
sets of lines run from the basement. I know I'm making a lot of
assumptions. What I'm trying to get at is, according to standard
plumbing practice (Northeast), should my assumptions be correct. I
know there is always the possibility that I get in there and find a
"why the hell did they do it THAT way" situation.

I'm really not worried about the water lines too much. My biggest
concern is possible issues with the drain. For example, any reason why
I can't just cap it and leave it there? The space above it will become
a closet.

I will probably get a plumber to come over and give an opinion before I
start. Just thought I'd check here first.