No idea about the rough running feeling, but what did she replace the transmission mount with? I replaced my factory mount, which is pretty soft, with a heavy duty poly mount that vibrated like crazy.
Does she have factory tires/suspension? A little suspension lift can put the driveline in a bind and cause vibrations when stopped and/or just as it starts moving.
I gather the symptom is strictly a rough idle, with the engine running well otherwise.
Checking for obvious vacuum leaks is a good place to start. Next thing to check is carbon build-up in the throttle body. Not much point in going any further until those two areas are known to be in good shape.
It’s been a while since I’ve seen her in person, but I think it might be raised a little. Maybe just the factory ‘up-country’ option. (She bought it used.) Wouldn’t vibrations caused by the suspension have cropped up earlier?
Her mechanic friend thinks it’s a vacuum leak, but couldn’t find one. I hadn’t thought about the throttle body.