In reference to question #4...

I recall running into this problem, having more than one pmd being referenced by a scene. I recall it causing certain iterations of a scene being inconsistent with morphs present or carried over. My memory is a bit vague on the particulars. I think I worked around it by creating master pmd INJ files that I would apply to new iterations of a "clean" target figure. Again, my memory is vague on this point.

There's a handy bit of software for general pmd manipulations found here... I have it and it's a useful utility, unique actually, for this type of thing.

Binary Morph Editor

That being said I hardly use it anymore, other than to take a quick peek at certain things, because

My final solution to all of this was to turn off external binary and embed the morphs as a general rule. I haven't found the overhead to be terribly bad, and I'm talking hundreds of custom morphs in many instances. As far as being centralized, the morphs are just as centralized embedded in a scene or cr2 as they are in an external pmd, and transparent to a standard text editor to boot. They're just not compressed. Note that I didn't do this because of some perceived boogeyman of pmd corruption, rather the selling point of pmd for scene files, compression, just became moot to me. It's still a godsend for INJ.

Those are my observations on that particular question.

I'd say that Charles Taylor (nerd) could give more informed, elegant answers to all of these questions, he's a mod on several Poser forums here. There's a chance he might not see the questions here, on the Poser Official, though.