TiVo is still shipping TCD649080 models with older software that causes this exact issue. The fix is simple:

-disconnect your upgrade kit
-reboot the unit, get it through setup, and get it connected to TiVo
-once the software has updated to 8.x, you can reinstall the upgrade kit

You may need to force some connections to TiVo to get the OS update download, and then you may need to restart the unit to get it to install.

Thanks! I'll try that as soon as I can.

Thanks!!!

I finally had a chance to try your suggestion last night, and it worked like a charm. All I had to do was unplug the power from the new drive and pull the master/slave jumper from the old drive. The Tivo booted and went through setup, came up in software 7.x (which also, unfortunately, required me to change my wireless-G access point from WPA to WEP for my Tivo wireless to work.) I had to force connection to Tivo two or three times before the software update downloaded -- I may have been impatient as I would go away, come back to a blank screen, get back to menus and reforce a download; then I discovered that it was still loading the previously downloaded stuff (the system information page showed % done/time left.)
After it finished the last time it showed "pending restart" in the system info.
I restarted and voila, software 8.3, with WPA support too. This morning I reconnected the upgrade drive (and put back the master/slave jumper on the A drive), booted, and I've got a 536-hour brand spankin' new Series 2 Tivo!
Thanks so much... as a 6+ year Tivo-head I truly appreciate your help!