Strange Windows behavior

Trying to cut a long story short, after a poor attempt at migrating windows from one HDD to another, it eventually culminated in my attempt to do a system repair (by typing something into the command prompt... I can't find the page that told me what to do now), which caused BSOD errors on restart. After much messing with recovery consoles and repair installations (repairs were hanging on "Installing devices") I've got Windows back, using this method (http://www.broadcastnewsroom.com/articles/viewarticle.jsp?id8658-3) then going into the F8 boot menu and selecting "Last Known Good Configuration" (not doing this results in more bluescreens, although safe mode works here). Safe mode seems to work fine (I'm posting this from safe mode), but in regular mode, things are definitely off.

I can log on fine, but after a slow start, MSN and Skype fail to connect. All other background tasks seem to start ok (Zone Alarm, Creative software etc). Any attempt however to run a program results in a brief second of disk activity, then nothing (task manager shows the programs in memory, but not actually doing anything). There is no connection to the internet (Network Connections in Control Panel shows the network as ok, but there is no "Internet Connection" icon like there usually is). Heading into 'My Computer', I find a whole partition missing off one of the hard drives. I am able to browse around the drives fine however. When you try and shut the computer down, you get a prompt about a program that isn't responding (seems to be random which one), which I acknowledge, and then nothing happens, forcing me to press the reset button.

I know it sounds weird, but maybe someone could offer advice? I'm going to try another repair installation and see what happens. I remember the steps I took to get to where I am now, so if it goes wrong again, I should be able to recover.

EDIT: Ok, nevermind. I've just switched back to normal mode, and everything is fine. Maybe the jolt of being in Safe Mode fixed it. Anyway, feel free to ignore me now!

So long as the drive letter assigned to the drive was the same in both instances you shouldn't run into any major problems - I guess you've found that out now. But for anyone else considering doing this, if the drive letters aren't the same then you are in for a major headache with the registry.