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ad 1) if your question is whether you can use OFR to break one big PDF file to many smaller ones and extract metadata out of them, then the answer is: yes, it is definitely possible. Note that since you work with A/R, OFR might be a bit overkill (your format is known, and perhaps, even modifiable, isn't it?), so WebCenter Capture might be sufficient
Nevertheless, myself, I would first ask the question: do we need this? You have one system, which out of data produces print-outs and one big PDF file, and now, you intend to construct another one, which will produce out of the big PDF - your original data (plus, the invoices, of course). Wouldn't it make more sense to modify the printing solution, so that it produces also small files with appropriate metadata as well?
ad 2) never heard of that, nor could find it in the documentation - as for printing, see 5.4.2. in http://docs.oracle.com/cd/E23943_01/user.1111/e12783/c05_viewing.htm#BCGFAGJG (it always mentions a document).
It is true, though, that UCM has Folios ( http://docs.oracle.com/cd/E23943_01/doc.1111/e10978/c09_folios.htm#CSMRC805 ) which have so called renderers, which might represent a single folio as a single representation (e.g. one large PDF). Maybe, you could customize your system and somehow re-use it in IPM.
ad 3) just read through http://docs.oracle.com/cd/E23943_01/admin.1111/e12782/c02_security.htm#CDDFFGGH In 126.96.36.199 it contains examples what roles can be defined.
ad 4) quite often discussed point. See e.g. Database storage vs. File system
As for partitioning, some kind of chronological approach usually helps. Note that it is very difficult to suggest anything without knowing how many data you have, and what your use cases are.