Installed VS 2003 and 2005 side by side again and had to do the treasure hunt through google to find all the little fixes to get it all working again, so thought I would consolidate them here.
After installing both:
1) Fix the registry keys so that IIS manager works again.
2) Unregister aspnet_isapi.dll in the v2.0.40301 directory under windows\microsoft.net with regsvr32 -u.
3) Re-register aspnet_isapi.dll in the v1.1.4322 direcoty with regsvr32.
4) Re-install iis from v1.1.4322 with aspnet_regiis -i
5) Reset IIS with iisreset.
After that, life was good with IIS, IIS management, VS web project creation and debugging.