So just to update, still don't know why endpoints are not downloading and installing the scanning agent. I downloaded it and deployed it myself with PDQ so my endpoints are protected, but I suspect the next time an update is released they are not going to get it automatically. We'll see. I haven't had any server trouble, support gave me a number of exclusions to set and that has been done. It was not happening too frequently, but it has been over a week since I had any issues so I'm hopeful that problem is resolved.
Workstations are a different story. Still seeing some performance issues there, I was experiencing them myself this morning. After any action there was a noticeable lag, especially when it came to opening a new tab in Chrome or launching a new browser window. I would see the Malwarebytes service spike in resource utilization briefly during this time and when it finished whatever it was doing the action would complete. I rebooted and haven't had any issues, but asking folks in the middle of design to reboot doesn't tend to go over well as it greatly disrupts their workflow and train of thought. I've added some exclusions to applications we use frequently on our workstations but still seeing this issue crop up from time to time. I'm going to test some more exclusions and see what happens.