Easiest for mine was to attach the motor mounts to the block first.
Also, do you have any need of that bad motor mount? Any interest of getting rid of it?
For the pilot bearing in the future: grease mixed with newspaper shreddings, fill the back of the bearing with the grease mixture, and tap a thick bolt in it. Hydraulic pressure will push the bearing out
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The motor mount I replaced on the driver's side is not bad. Because I happen to have a new spare, I replaced it. I would normally just keep it as a spare. I had to replace a broken driver's side motor mount on a Moab trip and it was NOT fun! The one I bought in Moab was NOT a direct fit and I had to lay on my back under my truck and grind holes with rat tail file for a long time!
On the pilot bearing, I tried the grease trick this time. I tried it the last time I did clutch job on my '85 and it didn't work for me then either.
I have suspicion that the pilot bearing has never been replaced. It was frozen and not turning, so I think that is why the tip of the input shaft is badly worn.