I use a AIO Repack that ricktendo made it include .net 1.1 to 4.0 with all hotfix included and it gives me no issues. I don't use SP4 tho. I use QFE + pos addon. There is a tool called .net clean up utility http://www.thewindowsclub.com/the-net-framework-removal-cleanup-tool
I might try to just remove it all and then try the solution that I use http://repacks.net/forum/viewtopic.php?f=6&t=26&sid=885d7e8be75f70d74e94f1ff93b2dc98&start=30