I'm far from an expert. But I do know that people cut major motion pictures on PPro. It must not be impossible, nor more difficult that other platforms. Just sayin'.
I suspect that the problem here is that you expect PPro to work similarly to FCP. From my reading (not experience) of FCP, this is probably not the case. They are different beasts, with different ways to work. Like most Adobe software, there are usually four or five ways to accomplish a given task, but some are easier than others. What one has to do, when learning Adobe, is to find and learn the easiest path. As you've found, that's easier said than done. I feel your pain -- the Adobe docs only teach you how the products work, not how to use them. A big fail, IMHO.
PPro doesn't seem to have a concept similar to "master project". That said, PPro seems to be perfectly happy to have as many sequences as you want in any given project, and as many bins (folders) as you want to organize your footage. I think of all my sequences as sub-projects, and work on them like that -- some shared clips, but usually not too many. In addition, these sequences can be nested, which allows a fair amount of flexibility.
I'm just thinking that maybe all you need to do is figure out how PPro wants you to work, and work that way, rather than trying force PPro to work the way you used to work in FCP. If you'll do that, your frustration level will drop and your productivity level will increase. At least, it has for me. But these programs are huge and complex, and learning them is like a lifetime experience.
I've never had Premiere Pro 'slow down' with the increasing size of a project, excepting the time it takes to load all the media, of course.
It might be a bit late now, but I think you should have done the entire edit on one project. Maybe next time...