One of the problems we came across during the last moments of testing for the CTP was a very rare situation where setup will tell you that it has failed, implying your screwed and will have a very messy setup. This is not what it seems at first :)
Specifically, this situation will only occur if you are asked to reboot after the CLR has been installed – something that doesn’t happen very often. When it does reboot there is a bug in setup that accidentally deletes some of the files setup needs to continue (Specifically the J# runtime installer), so it thinks that’s something has gone horribly wrong and errors out – DON’T PANIC!
When setup tells you it’s failed, ignore it. Click out of the failure and return to the 3-step step setup dialog. Click setup again and keep working through setup as before and it will install fine and dandy this time.
This will be fixed for Beta 1 of Whidbey I’m told – we caught it a little too late and didn’t want to put the CTP at risk from code churn. Additionally, it seems to rarely happen, so shouldn’t effect too many people. If it does, let me know (comments, mail, IM)