There are compelling reasons why the vehicle would raise suspicion, but can someone please tell me if there is a record of when a licence # has been pulled over? If so, then surely the office next pulling over the vehicle knows this when they punch in the licence #?
At some point, it becomes unreasonable. I think this "some point" has come to pass. I would go to my nearest detachment and voice my concerns and ask for a note to be placed on file, if possible. This many times in such a short period, if it were happening to me, would be worrisome, and as a citizen sharing the road with others, with no criminal record or associations, I would consider it harassment if it didn't stop and file a complaint with the board. I am appreciative of Metro doing their job as is obvious here, but now it is overkill and the OP needs to be left in peace. He's earned it, and surely, there has been enough police contact to know that his story checks out.
Unless of course, something very crucial to this story has been omitted.