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I would not back the nut off to align the nut with the cotter pinhole. Doing so can result in the taper between the knuckle and the tierod becoming loose. The cotter pin would keep the nut from backing off but it would not prevent the tapered shaft of the tierod from spinning in the tapered hole of the knuckle. As @MikeSaull has suggested lube the threads. ...

I would use some anti-seize on the threads then tighten it to torque spec. If it doesn't line up then I would tighten it until it does. This is just what I would do. If it is a weak bolt or a really bad place for the threads to strip then I would just loosen it until it lines up. Once the cotter pin is in it shouldn't go anywhere anyways.

Base on the limited information it's sounds like the tranny could be out of spec. This with new fluid would cause a pronounced vibration. Try to find out what fluids were use and if the torque converter was also serviced or replaced. As said, the new motor mounts would make matters worse as it puts more pressure on the rest of the parts. If these are poly or ...

When you brought the Jeep in did you explain that you have a vibration? If you did and they suggested a tune-up was in order, you have a case to bring it back and complain. I donot believe it is related to the motor mount change,suspension or transmission work. The reason the vibration lessens when out of gear is beacause the load is removed. I think it is ...

It's probably just the new motor mounts. If the new motor mounts are stiffer you will get more chassis vibration. I am a little surprised that shifting to neutral effects the vibration though. Is it automatic? Did they have to drop your transmission cross member or any drive shafts during the service. If so it could be something to do with that.