Cebain: are you sure you have VC 1.6 and not 1.5 as well the full version, not the upgrade, or tial version?
Also, I know you just said so, but just to cover all bases... when you are done w/ the upgrade, and do the hard reset (it appears you are doing that right), are you SURE you are soft resetting BEFORE the 'customization' (Extended rom) even BEGINS?
As soon as I see the countdown I get 'er done. I once did my soft reset about 2 seconds into the customizations and my phone ran like... well it didn't run well and I had to hard reset before I could really get going.
Sardinour: are you familiar with sk tools? The trial (same as retail file) has the limitation of only 6 entries in any of there lists are shown (really works enough for those of us that keep a tight machine). Anyway my point is particularly in the 'invalid registry enties/values'. It seems that there are some things in there that may run better if they were complete, or removed.
One of the first things I do w/ I load a rom (after a couple boots and real basic settings) is to run SKTools. I know it won't find things like the extra space in sp2, but it does show entries that seem to be referencing invalid objects. Specifically 'COM object registration info' and 'System drivers (built in and PCMCIA' as well as there seem to be some 'Empty keys'.
While I have already done some slight pruning, I would guess you may be able to do a little more, and that may add to stability, these are probably leftover from previous build revisions at MS or the original carriers tweaks.
You can find the latest at
www.s-k-tools.com .