1. That's less a matter of being digestible by Perl; all Perl constructs except a number of functions geared towards Unix specifics work everywhere. See perlport.
2. Windows doesn't use the shebang line at all, although perl examines it after launch. You may run into with issues with "too late for -T".
3. I would suggest you deliver two versions, at least for Windows users: an unbundled one and one built with PAR. The download page should suggest them to get the PAR'd one unless they know why they'd want the other. I don't see a need to write module fetching tutorials for the unbundled package then. Consider wrapping the Windows PAR version in an InstallShield-ish installer - I quite liked the NullSoft installer creator, myself. Due to XS modules, a PAR'd version for people on *nixoid systems would be difficult to offer; you'll need to account for a lot of systems.
4. I'm not sure what that question means. The quoting mechanisms are very different, at any rate. I'm not sure the MS shells even offer sufficiently powerful escaping mechanisms to deal with arbitrary data. sh type shells do - clumsy ones, but they don't impose restrictions.
5. I don't think there's anything specific about those. You will have to look into binmode though. (This is a no-op on *nixoid systems, so you don't need to maintain two different versions.) In other notes, remember that MS systems don't pay attention to capitalization in filenames.

Makeshifts last the longest.