Have you tried printing directly from Indesign?

Not talking to the printer sounds like a bad idea if you are to be responsible for the outcome.

I would advise you to talk to your print supplier as it is they who will be doing the print and finish, they will tell you exactly what they need from you.

Use the book function, from a workflow point of view I would consider it foolhardy to do this as one document whether in Quark or Indesign. Do it as sepearate parts and manage it with the book function.

Sounds like rather than software skills it is time to look at this as a design issue. You refer to the baseline but setting that comes from you deciding what the leading is going to be. I could put forward 10pt type on 13pt leading as a good example, but here google is your friend, look up leading and type size, and I suggest some extra reading on grids and book design.

Cheers and I trust you enjoy the world of type design.

You need to include the slug area.