It looks like this was a combination of the upgrade,
increasing use of ASP files and not having seperate application
pools in IIS.
We've just starting edding aspx apps, previously we only had
one asp app so we only used the default app;icaton pool in iis.
With the errors in the virtual directory started, we deleted and
remade the VD with it's only application pool. That appears to have
resolved the issues. The only concern I have is one of the VD did
have it's own applicaton pool and still had the very slow response
after the upgrade. But I'll see how this solution works for the
future.
The decesion was made to only have cf8 installed since that
worked well on our testing server, so we did intend to overwrite
the CFIDE folder.
Thanks for checking this out and for your time on this.
At this point I consider this closed. If something else comes
up I'll start a new thread on it.