This has been quite an exploration but it seems we are emerging from a "stuck" Joomla install.
Joomla 1.6, upon which the last TKL generation was built, has been left somewhat to the dustbins by the Joomla community. Several extensions have stopped to work with it and it is difficult to find usable upgrade paths (except in my downloads folder).
Unfortunately, my Joomla build stopped taking normal Admin Updates and though I have found many other ways now to grab an old snapshot and get "an update" I really needed some true "in line" updates to work.
After many attempts (where the upgrade ended in an error "cannot copy file") I realized that several of my files that were living on the server were being owned by "root" rather than "www-data". Simply changing permissions (via Admin Tools) is not enough to fix this. Changing Ownership for the folder got the Inline update to work.
This command does the trick and is often helpful in TKL upgrades and maintenance work:
chown -R www-data:www-data /var/www/joomla
I have been able now to upgrade sequentially to Joomla 1.6.6 (a while ago), then 1.7 today, then finally 2.5.8 today (which seems to be the last stable 2.5 build).
Lucid build at Joomla 2.5.8, should be backed up with TKLBAM,
To migrate the the TKL 11 Lucid (Joomla 1.6 Ap) build to TKL to the TKL 12 Squeeze Build (Joomla 2.5 Ap) you need to do a fresh TKL Joomla 2.5 install. This gives you a Joomla 2.5.4 system at startup so it is important to update (via your Joomla Admin panel - updates) to Joomla 2.5.8 so that it is the same as the TKL Lucid Joomla I am migrating from.. You should run your TKL security updates after you set your proper IP address for your system. IP's, DNS and SSL deserves a whole How To actually, but for now, if you are using the same IP just turn the Lucid build off after you have done the backup and have the squeeze install use the address, you can also use 2 different IP's which won't matter as long as your DNS is setup properly and you don't have issues with misnamed SSL certificates. DO NOT LEAVE THEM BOTH RUNNING WITH THE SAME IP ADDRESS in every event!
Having the otherwise empty Squeeze (Debian) Joomla 2.5 build to 2.5.8, next, initialize tklbam (easiest through WEBMIN for me) , then run a TKL-BAM Restore (all very easy within Webmin). Backup and Restore both take a while, but once done, simply restart your system and you should have fully migrated Joomla systems that can move forward in the TKL ecosystem.
Trick here: keep your passwords the same on Debian Squeeze 12 that you had on Ubuntu and things run well. After that you can mess with your passwords, but you won't have a working system unless both systems are synched to beging with.
Final steps involve simple restart and then getting down to business. Upgrading to Joomla 3.0 I am sure will bring a full new set of issues. Numbered Bullet points might help these explanations.