Buy a couple of gallons of solvent to clean all the parts up.
Use a pilot bearing pulling tool to remove the pilot bearing. Then you don't need to remove the flywheel. Use the old pilot bearing to drive the new one in.
Most clutch kits come with a plastic clutch alignment tool.
Remove the steering box when you adjust the clutch so you can see exactly what the throwout bearing is doing and adjust it precisely. You'll need a tie-rod remover "pickle fork". While you have the steering box on the bench, it is a good time to clean it up and go through the adjustment procedure. I found that I was able to remove A LOT of lost motion from my steering box just by adjusting it. I had previously thought I'd have to replace the box, but it turned out there was no need to. Remember that the top of the box goes back on with the threaded ears toward the rear, and that the steering arms will go on the sector shafts only 4 ways, in 90-degree increments. Carefully note the locations of the steering arms before you remove them, and make sure you re-install the sector shafts so the steering arms will go back on in the same locations. If the steering arms are loose on the sector shafts, take the arms and shafts to a machine shop and have the splines cleaned up.
Removing the steering box will also let you turn the tranny input shaft by hand until its splines mate with those in the clutch disc, and to see exactly when they do. If you don't do this, it can be very difficult to get the input shaft to enter the disc without possibly damaging the disc.
I used two come-alongs attached to the rafters to remove the hood; one in the front and one in the back. This makes handling the hood really convenient. You can just lift the hood 'way up in the air and leave it there until you're ready to lower it; and when you do lower it, you can adjust the angle just right so it will slide over the instrument panel nicely.
Chase the threads on all the bolts and bolt holes before you replace them, and use anti-seize.
Take pictures as you go, and make notes of where all the different bolts go.
Threading the long bolts into the bell housing temporarily does make it easier to mate the transmission and engine, but remember that you still have to get the engine and tranny perfectly level and parallel side-to-side before they'll mate. You can swing the tranny from side to side by pushing on one rear wheel as you pull on the other.
The engine will want to tip over to the right side when you split it from the tranny. You will need to either wedge it upright, or attach a rope to something on the right side to pull and hold it upright.