For the overhauling ships...cancel the overhaul...there is a command-it might be "abandon overhaul" then advance the time 5 min or so, if that doesn't work turn on SM mode, delete the ships and then recreate them. I'd also remove the commanders first since I'm far from sure what happens to them in that case. There are issues with overhauls, for one thing if you need to repair a ship and overhaul it put it into shipyard for repair first then give the overhaul command.
For the mass driver, if it is loaded on a freighter just give the freighter the "unload mass driver" command and it should show up in orbit when the frieghter is done, it will take several days to unload. I may be missunderstanding the problem you are having howerver.