I was able to fix this. First, I backed up everything. Then I disabled the multi-site network and deleted the plugin on the main site. When I enabled the multi-site network, the plugin was gone and the other sites were working fine.
I probably installed this plugin before I set up the network. I hadn’t noticed any problems until I tried to disable it after the 4.5 upgrade. The Customize area was not working and I was checking all the plugins. Since I was able to delete the plugin, the Customize area now works correctly.