I would have fewer worries restarting a GA645 than any other camera - because its counter detects the film starting and is consistent to within 1/10mm from frame to frame. But the bulge issue remains.
The spots are, has been said, spatter from somewhere in the atmosphere. Harmless to the camera and to your pictures. Use a UV filter if you don't want them on your lens (you will still have to clean the filter periodically, but that is less stressful).
They will wipe off, but if you do it incorrectly (do not simply use an old microfiber cloth that has been sitting around), you can scratch the lens. Use a camel hair brush to get all the dust off the lens, breathe on it and hit the spots with a clean cotton swab. Do not use paper products.
The instruction manual for this camera is online at butkus, and there are a lot of things about this camera that will be difficult to learn by trial and error.
Enjoy the GA645! It is one of the coolest medium format cameras made.
Dante