Short version is this: I have a very clean reinstall of the latest version, but admin screens are taking 5 to 20 minutes to load. Need help figuring out how to debug.
Long version with details:
Following some recent security concerns, a client had me do a clean re-install of WordPress on IIS7/Windows 2008 R2 this weekend.
I first upgraded their existing installation, version 3.5.something, to 3.6.1 (to make sure there'd be no db compatibility problems when I did the clean reinstall). Then U backed up the database, wiped the existing WP filesystem, and installed a fresh download of 3.6.1, restoring the wp-config.php from the old installation so that the new installation would use the existing database.
After the upgrade of the existing site, the admin became INCREDIBLY slow. At first I was getting code 500 errors, the details of which proved to be either "php-cgi.exe the fastcgi process exceeded configured activity timeout" or "php-cgi.exe the fastcgi process exceeded configured request timeout" errors. I changed both of those settings in IIS7 FastCGI Settings, and now I have activity timeout & request timeouts of 1200 seconds (20 minutes!!) so I can use the site, but most clicks in admin take 3-5 minutes and a few seem to take much longer (as I write this, I've been waiting at least half an hour for a click to my Plugins admin page to come through). I had thought that whatever the problem was would go away when I did the clean reinstall, but it did not.
How can I pinpoint where the problem is? I don't know how to drill down beyond the point of "well, it's something in the admin." All the forum posts I've read on slow admins say things like "install fresh" or "deactivate all your plugins." I've done all that, basically, in the course of what I was trying to do in the first place (I will say that I didn't deactivate plugins in the existing installation before I blew it away, so if the db is expecting any of them to be there, it's not finding them). The only bits of my existing site currently in place are the old db, wp-config.php, web.config, blogs.dir, and one custom theme & one custom plug-in that apply only to the public-facing site—which, again, is fine: this slowness is ONLY with the admin.
This is on a dedicated server to which I have remote desktop access; there's nothing weird happening like a redlined CPU in the Task Manager process monitor or anything like that.
I don't know if it could be related but I did have a couple of small problems with upgrading the existing installation to 3.6.1, around getting an error using the UI-based upgrade tool to the effect of there was no temp directory to write to, so I created one, specified it in the wp-config.php, and that did get me upgraded although then at that point I was instantly dealing with those 500 errors.
That's all I can think of to share for diagnostics—I'd be so grateful for some help, because I've been parked in this exact chair for about 26 hours now, minus last night's sleep break, trying to finish this job.