First, get a better programming resource. Two very good books to learn Perl are Learning Perl and Programming Perl, both by O'Reilly. The latter is oriented towards those who already have a programming background, so it may not be a good one for you. I don't know the book you mention, but the "in 21 days" part makes me suspicious whether it's any good. Look in the Reviews section here in the monastery for some good reviews of existing Perl books.

Second, this "Perl scripting tool" doesn't sound like a full Perl implementation. For a Windows platform, I use ActiveState's Perl implementation. There are others, including IndigoPerl from IndigoStar, but I've never used it, so I can't vouch for it.

Some of your other questions:

• Yes, most Perl programs will run on any platform, but some functions don't work the same everywhere. ActiveState's documentation has a list of "this works, this doesn't" on Win32.
• The monastery is an excellent resource (IMHO ;-) for those learning Perl. Whether a book, the docs themselves, a course, or an online tutorial will work better depends entirely on you. There are Perl books specifically for system admins, but I think those are more oriented towards Unix/Linux admins, like Perl for system adminstration, which is multi-platform. You can find some very good resources on Perl for Win32 admin at http://www.roth.net.
• I have no idea what the orphaned home directory script is, so I can't say anything there.

Anyways, Welcome to the monastery! Make yourself at home. Read the FAQs and don't be embarassed to ask questions. (Oh yeah, read the Writeup Formatting Tips. ;-)

Update
Added links to books.

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