After figuring out today that most of my problems were self induced, I feel I need to explain myself a bit.
Don't get me wrong. I've been very impressed with the features and improvements that have been made in the past few months of this extension, and honestly, the extension itself. I can't think of any other extension that is more essential than this one.
However, even considering the issues on my end, Akeeba still seems to dangle the "golden carrot" of straight-forward directory-to-directory copying of archives. Ideally, the point of the "discover and import" feature should be to completely eliminate the need for the kickstart and moving any files around by FTP (within the same web server). Akeeba does such a stellar job at backing up files and databases, it should be easier to use those archives (Again, within the same web server. I have several sites that share the same disk space). I do think you guys are on the right track, though, given the vast progress made on this usability in such short time, I just need to be patient, and/or learn more.
So, that being said, most of my headache was self induced by my own ignorance in the following ways:
1. I was specifically trying to avoid downloading the archive files and re-uploading them to the proper site's backup directories via FTP because they were each about 4 GB in size and would have taken 4 hours to download on my 3 M bps connection, and then another 6 or so to upload to the other site, plus time for Akeeba to work at restoring. It didn't occur to me until today, that 4 GB is probably unusually large for my website. After looking at the files on the server realized that I had uploaded a 3.8Gb zip file sometime in the past, for someone to download, and did not remove it. Therefore, it was being included in the backup archive This would have been counter-intuitive to being able to Akeeba just being able to see a file that is on the same server as itself. I kept telling myself it would be faster to simply FTP download the entire Joomla installation and backup the database, and copy them over to the dev site manually, but that was only because I didn't realize that file was there.
2. Which brings me to the second glaring issue. My measly 3 M bps connection. Last night I upgraded my service to 24 M bps so, I shouldn't have a problem downloading/uploading 4gig archives should I need to in the future, but I won't now that I realize I have to exclude the 3.8gig zip file from back-up.
Anyway, thanks all for your time and patience, and work on this great extension!