Sometimes the VST scan would take several minutes. It seems like before the upgrade it was scanning my whole computer but it eventually found all my instruments. Is there a way to turn this setting back on? I was eventually able to manually add most of my soft synths.

I have had the same issue lately.  i purchased new plugins and after a scan Sonar did not see most of my VST3 stuff.   I deleted all the old scan locations and added them back in.  It took a couple of tries and eventually everything got added back in.  Kinda scary for a hour or so.
 

I suggest checking out the documentation for the plug-in manager. It's the key to scanning, excluding plug-ins, rescanning failed plug-ins, creating custom layouts, etc.