performance problems after 2.86 upgrade? (cpanel)

Hi, I run a site with medium traffic (6000 hits a day, 11,000 posts total) that’s been on wordpress for over 5 years. I’ve been the system admin for most of that time.

After upgrading to 2.86, we’ve been experience performance issues. It causes the cpu to max out on our server, causing restarts of mysql. It has started after the upgrade.

I’ve benchmarked it with firebug and see some static resources that are taking a while. But I’m also seeing that the main GET call is taking a long time (usually over 7 seconds).

but I don’t even know how to begin troubleshooting it. i’ve looked over here https://codex.www.ads-software.com/WordPress_Optimization. My hosting service has cpanel, but without a shell account.

1)there’s an off chance I may have uploaded the files for the upgrade incorrectly. I used cpanel to upload the files instead of ftp (for a long and complicated reason I can’t go into). It’s possible that I may have made a mistake manually uploading something (even though I double-checked and triplechecked what I did), and the blog itself seems to function without errors.

2)plugin performance problems. We have 20 plugins running: AdSense Manager, Akismet, All in One SEO Pack, Blogroll Links Widgets, Category Order, Collapsible Archive Widget, Configure SMTP, Exclude Pages from Navigation, FeedBurner FeedSmith, Full Text Feed, Global Translator, Google Ajax Search, iWPhone, Live Comment Preview, Ozh’ Who Sees Ads, Recent Comments Widget, Sociable, Subscribe To Comments, tagaroo, WP-Poll,s WP-Stats, WP Super Cache. All are current except wp-stats, which had an update a few weeks ago.

Unfortunately, the site editor wants all the plugins.

3. wp-super-cache. We’ve been using this for a year.

4. a web resource in a widget. for example, I noticed in firebug that mybloglog widget is taking up a lot of time, so I axed the sucker.

5. webhosting issues. It’s a huge cpanel site, so I suspect system resources are managed pretty well.

first, are there any likely suspects here?
second, am i correct in assuming that the upgrade/replacement of files via cpanel must have worked (or else wordpress would have complained immediately after!?)

third, can firebug provide any clue as to which plugin is dragging things down?

other than stopping and starting plugins, i don’t have any methods for benchmarking plugins on a live site. Any ideas? I have a local install somewhere, but I’m afraid that benchmarking a local version won’t be an accurate simulation.

Thanks for your help.