The thumping can happen once in a while - generally if the head has been moved manually from the starting position in the upper left hand corner.
If you let the machine move to the correct position after cuts, it finds home all on it’s own. If you move the head for cleaning while the machine is off, or when removing material, it’s going to thump. The startup routine expects it to be in a certain place, and if it’s close to that place but a little too far left…that’s when the stepper motor thumping happens.
(It really doesn’t hurt anything, although it sounds awful, and it’s not something you want to do with every print, but it’s better for you to let it finish without turning off the machine halfway through.)
If the head is right underneath the camera when the unit is powered on, the first picture taken relays that information to Glowforge and they don’t use the standard startup. That’s why moving the head under the lid camera works. But I haven’t found it necessary to keep doing it. Usually doing it once after the machine has been turned off corrects the situation.
Just don’t move the head by hand any more than you need to, move it slowly when you do, and never when the machine is turned on.
As far as the calibrating taking a long time - that can have several causes. If it gets stuck, just turn off the machine, give it a minute and try again. If that still doesn’t fix it, reboot by holding the start button down for ten seconds until it turns teal, then turn off the machine, move the head into position under the lid camera, and turn it back on. That usually clears it.
If it doesn’t, the support group can usually pinpoint a problem from their end, but they will need more information from you about your browser and connections, so it’s a good idea to read through the Troubleshooting Tips section at the Support button on the app.
Finally, there are times when they are working on something on their end when everybody experiences some lags… it’s not something that tends to last for long, so for now, I just work around them. (Part and parcel of getting the units up front, and I’d much rather have it so I can play between the hiccups.)