Importing Mailboxes Upon Hard-Drive Wipe and OS Reinstall + .Mac Issues

Hi --
I was wondering if someone could help me out here. My dilemma is this: Long story short, I had to have my hard-drive wiped and have Tiger reinstalled yesterday at an Apple Store. Beforehand, I copied my entire Mail folder over to my external drive. Now, after the reinstall, I've reimported all of the mailboxes, and I'm not happy with the way things are looking. I should note that I used a mac.com POP account, in addition to another POP account, the setup of said account now apparently also having been wiped in the reinstall. Anyway, here's the breakdown:
(1) My entire Inbox is imported, but appearing inside of a grey "INBOX" folder inside of an "Import" folder, on the mailboxes strip. I've tried dragging the entirety of the Inbox contents up to the REAL Inbox (the very top icon) which is where I've always had my Inbox contents, and where I demand they stay!! However, doing the aforementioned copy/move, which seems like a reasonable enough action, leads to the following problem:
(2) It seems as though Apple Mail is now UPLOADING the entirety of my Inbox back to the POP web server, so that if I check my mac.com account via .Mac on the Web, all of these old messages from 2003 are showing up in the hundreds. (a) I do not want Mail uploading any old messages of mine ANYWHERE. Not even to my old account. (b) Because I've got about 40,000 messages in my Inbox, I do not want these going back up onto the server, taking up all of my space.
(3) I would also like the proper "Sent" (paper-airplane) box at the top to contain all of my old sent messages, and not some "Sent Messages" mailbox-folder of the sort in which it has currently dumped all of them during the import.
(4) Just as a lateral question to the above, I'd be very grateful for any tips on Preferences settings or the like that might get me out of the above POP quandaries. It seems as though there are options for "Do Not Store Sent Mail on the Server!" but no preference for "DO NOT REUPLOAD THE ENTIRETY OF MY INBOX TO MY POP ACCOUNT'S ONLINE STORAGE UPON A REIMPORT"!
Anyway, many thanks for any help anyone can provide on these matters!!!
best,
craig keller.
Power Mac G5   Mac OS X (10.4.9)  

Hi David.
Thanks for the helpful information. I had an inkling that the .plist Mail file might have been the cause after all of this happened, but had no idea it was necessary before the fact -- which of course is partly-my-fault, partly-the-world's. (As I see it.) So, the .plist file is gone, but my messages still exist, inbox, outbox, and all of the mailboxes.
In the meantime, where I'm at is the following juncture: What can I do to make a boot-up of Mail CEASE uploading the OLD contents of my Inbox onto the online server (and my apologies for the confusion in the IMAP/POP nomenclature, it's all a blur to me), which occurs automatically upon opening Mail -- the program is hanging up, with the "pie-chart" icon appearing to the left of the Inbox, not downloading any mail and so on, as it (silently, secretly, invisibly) uploads my Inbox to my IMAP .Mac webmail Inbox. Of course, this would not be an issue, as I could ostensibly just go on the Web and delete all of this old excess mail, were it not for the fact that I have 250MB of storage free on said .Mac account, and approximately 1.06GB of Inbox mail associated with that account, accumulated over four years of daily use.
I should also note that even if it was a "bad idea" for me to move my messages back to the Inbox, and if it shouldn't be used for archiving purposes, that is -exactly- what I use it for, as it's simply the place where my mail comes in, and traditionally, the online web server deletes mail after X number of days sitting there; that done, it still, nevertheless, exists within my Inbox. Where my mail comes in, that's where I want it to stay. No moves, no folderizing beyond that. The Inbox is the Inbox, and that should be that. (Pull the messages from the server; keep copies on the server for 10 days or whatever, then delete; but let the messages exist, still, on my hard-drive, on my computer.) Sorry if I'm conceiving of this contrary to Apple's dicta, but it's operated exactly the way I've needed it to -- until now. So I'm a bit frustrated; also slightly miffed by the fact that I was told to post on this forum from Apple, rather than getting a human-to-human, real-time interaction on the matter, as that, apparently, costs $49.99 for a 30-day trial.
Anyway, any further help/insight you (or anyone else) might be able to provide on the matter would be GREATLY appreciated!!!!!!! As I'm sure it is with so many, my mailbox inbox is the core of my life, and I like it to be "just so" -- possibly a foolish idyll on my part, but there you have it.
thanks!
craig.

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