Not sure if this will be helpful for anyone or not, but here goes...
I downloaded the updates from the website, and the backed up my settings (all settings and triggers only).
I then went through the installation instructions step by step (don't forget to HOLD the REC button while starting the install of the Boot loader file (I THINK that's the only one that "needs" it, but I did it for all).
I got to the Sound update, and it failed TWICE! (Yikes!)
So I RE-downloaded the updates, unzipped them again, and re-did the updates, (All of them), and the second time it all went fine. (So don't panic if it crashes like mine did!)
My set SEEMS to be working fine, not sure if it's any better yet or not, but it's not any worse.
I do still have the TOM1 issue, however.
(As soon as I have time, I will address the Tom1 issue with Alesis, but won't until after Memorial Day... big project going on, and just don't have the time during the week to call them yet.)