It's unlikely that over-torquing the mounting bolts would create problems, since the ends of the mounts are isolated by the big rubber puck - you can't preload the rubber. Unless you somehow damaged the trans mount when you jacked up your engine, I can't think of what would be wrong. Replacing the mounts is so straightforward, there must be something you've overlooked.

When I do mounts, the passenger side I can change easily enough, but for the driver's side I usually unbolt the whole bracket from the engine. If you did the same, did you fully re-bolt the bracket? It sounds like somehow you have metal-to-metal contact instead of metal-to-rubber-to-metal. I also don't think you can interchange left and right mounts, although I suppose that's possible.

Take a look from the passenger side of the engine, down at the alternator and oil filter area. Is the oil filter resting on the front crossmember? If it is then your replacement mount may have failed.