I don't know if it is safe to hoist the engine using the gap in between cylinders 2 and 4 as the lifting point. Keep in mind that these four bangers weigh around 600 pounds.
Oh, something that is VERY important. The 1/2" head bolts DO NOT
have 13 threads per inch. They have 12
BTW, no rubber on the engine or transmission mounts.
If it were me, I'd put the engine on a stand, take off the oil pan, and do an inspection before dropping the engine into the truck. Here's why I would do this:
1. On Justin (my '28 Canopy Express), the previous owner assembled the engine after the block got done at the machinist shop. ALL the bearing caps were just finger tight! Luckily, they had cotter pins on the nuts, but imagine what would've happened if the pins were not there (shudder). This discovery let me to adjusting the bearing caps (removing or adding shims) to get the proper clearance around the crankshaft and tightening the bearing caps before putting the cotter pins in.
2. Having the oil pan off is a great opportunity to make sure that all the oil reservoirs that feed the cam and main bearings are clean and not full of sludge. Again, Justin's reservoirs were full of crud, so I don't have a lot of respect for the machine shop that worked on the block or the mechanical ability of the previous owner.
3. A new set of oil pan gaskets (either store bought or homemade) will help in preventing oil leakage. Getting the gaskets to stay in place around the front and rear main bearing caps is challenging. Here's what I do to make it work: https://vccachat.org/ubbthreads.php/topics/394210/re-resurrecting-a-28-4-banger.html#Post394210
4. Make sure the little wedge-shaped cover plates are in place to cover the gap between the flywheel cover and the block. For more info, read this part of my engine rebuild adventure from 2017: https://vccachat.org/ubbthreads.php/topics/400512/re-resurrecting-a-28-4-banger.html#Post400512
5. Check that the oil troughs in the oil pan are positioned properly so that the tangs on the rod caps actually dip into the troughs to create the oil mist that is necessary for all the internal oiling of the engine. Here's the procedure I followed for Lurch's engine: https://vccachat.org/ubbthreads.php/topics/394209/re-resurrecting-a-28-4-banger.html#Post394209
6. Who knows how long this engine has been sitting after it was rebuilt. While the oil pan is off, I suggest squirting some 10-30W oil around all the bearings before closing up the bottom end and smearing some assembly grease around the cam lobes.
Aside from the above stuff about the bottom end, make sure that all bolt threads that go through the block and stick into the 'splash zone' of the oil mist have some thread sealer on them. I used Permetex #3.
Has the pilot bearing been replaced? Maybe stick a new one in there just to be safe.
Regarding the alignment of the clutch, I seem to remember that a wood pilot bearing tool from an AD pickup is the correct size for the old four bangers. ;-)
Does your truck have the original carbon plate throwout bearing? I suggest replacing it with a newer-style permanently sealed ball bearing type of throwout bearing. The carbon disks tended to overheat and cause issues. The newer style definitely gives you peace of mind against this problem.
When you put the transmission in place, it will be loose between the chassis rails. There are 1/8" shim plates that drop down over the mounting bolts that will take up the slack and make for a tight fit. See the pic below for a view of the shims I'm talking about.
Speaking of putting the tranny in, make sure the truck is up on jack stands and the rear stands are supporting the chassis, not the rear axle. This will allow the rear end to hang down far enough to provide more space for getting the u-joint bolted together. This goes for any vehicle that has a torque tube.
That's all that I can think of at the moment.