Thought it was resolved, and it is for most but one pool is still having problems, it seems we one site in a pool causing near 100% cpu use that is causing this problem, even before the reboot.
ASP pages are loading properly, ASP.NET pages in this one pool may be slow, we are working to sort it out and notify the abuser of the issue.
We are still working on this, asp.net pages are still loading slowly in this pool, it is also slowing us on the server side as well, even after the reboot.
I am going to have to stop this pool as it is causing so many problems for other pools on the server making them slow, and making me tracing the abuse near impossible.
I will be moving all sites out of this pools into 3 other pools and testing them seperate.