I just realized I never reported back to these issues I was having. The "Resuming the auto guider" issue was fixed just by me changing the settling options in SGP. I change the "settle at <" setting to 1 and for 5 seconds and now SGP never hangs up when Resuming the auto guider.
For the other issue it turns out that the CEM60's DEC saddle hub was the problem. I unplugged my ASI120MC from the DEC saddle hub, that I use for a guidecam, and now SGP doesn't go unresponsive when doing autofocus. I believe the CEM60's hub couldn't handle powering the ASI120MC and a TemperHUM device, while transmitting data from everything, especially when downloading an image from my DSLR. Thats why SGP would freeze when trying to download an autofocus image.