I have a server that is currently running 3.2.2, 3.3.7 and 4.4.1 on different sites.  On the same server I am also running MSDE and SQL Server Express.  I've essentially been doing the same thing you mention in trying to keep the old site running while I move it to the new version.  I especially ran into problems upgrading from 3.2.2 to version 4.x, so it was better to create the new 4.x sites as new installations using templates exported from 3.2.2 and 3.3.7.  It was a bit slow and tedious, but it would have been even more tedious if I had to retype entire sites from scratch.

Hello..

Can you describe how you did the 4.4.1 upgrade to 4.5?  I have tried numerous things and each time is worse than before.  I would rather not have to do a complete re-install...and would like to do an upgrade.  Any help would be appreciated.

I'm reading this forum looking for an answer to the same question - almost. I have both a 4.3 and a 3.3 site to upgrade.