Harry,
I am happy that you asked about bolts. This has been a confusing issue to me. To quote the instructions from part #759-3952, the CCC part number for the OEM ISO mount: "Reassemble engine iso/mount using previously removed bolt and new 3/8" lock nut. Refer to parts catalog for proper hardware. Torque nut to 100 inch-lbs (8 foot-pounds). Do Not over-torque."
I removed 3/8' x 2 1/4" bolts. The PO had put in anything from no grade to grade 8 bolts and they were not in good condition. I chose to replace the bolts with new 2 1/4" bolts from Caterpillar, only to find that during assembly the bolts were rather short, exposing just a little thread at a loose position. I thought these bolts were too short, and I removed them and exchanged the 2 1/4" bolts for 2 3/4" bolts. I then tightened the lock nut to 100 inch-pounds. There was well over 1/2" of thread showing when 100 inch-pounds of torque was achieved. I thought that was a lot of thread to be exposed, and I looked at the snubbers and found them to be against the lower frame flange. I then removed the 2/3/4" bolts and stopped to research the correct answer.
I will reinstall the engine cradle and 2 1/4" bolts and tighten to a couple of threads showing on each corner as recommended. I expect to have ample pressure on the ISO mounts and am unsure as to the clearance of the snubbers from the lower frame flange will be using 2 1/4" bolts.
Perhaps I should go back to Caterpillar and get 2 1/2" bolts to continue with the experiment. You, Jeremiah, and a couple of others have recommended that there be a little bounce in the rubber mounts, and another mechanic has recommended that the ISO mounts be rather tight. It makes sense to me that the snubber be available to absorb some of the shock with PTO engagement. Currently, I have no shims between the snubber and the cradle. If I knew the correct answer I would be in the shop putting together this thing, rather than looking here for some guidance.
I wish I thought like a mechanic.