I think you probably could see it, I know when the harmonic balancer slipped on my '98 Jeep 4.0 it was pretty obvious. As long as you have water hooked up you could run it at idle but the exhaust water would be shooting all over you trying to see the coupler thru the gimble bearing lol.
when the shop installed the engine did the use your old coupler, or a new one?
never had vibs in the past?
other thoughts...u joints, but I'd think if they were bad you'd also hear noise, and would have heard it before you swapped engines.