Apply a liberal amount of wheel bearing grease to the inside of the pilot bushing/bearing, you don't want any outside of the bearing.
Resist the temptation to grease the splines- use a dry graphite spray lube on them. Any grease on the rotating assemblies stands the chance of being thrown off onto the friction surfaces.
Get a GOOD clutch alignment tool- most of the universal/plastic ones leave a lot to be desired. I use an old input shaft. In a pinch, (I'm assuming this is all out of the car) you can carefully use the transmission (sans bellhousing) to align the clutch disc, but it's awkward- so be careful.
Use the graphite on the input collar/throwout bearing interface, too. A dab of grease on the clutch fork fingers where they contact the T.O. bearing, and a dab on the pivot.
Bolt the bell to the trans, and assemble your T.O. bearing and fork; then slide the trans/bell assembly into position on the engine. As said, use your driveshaft yoke to turn the trans a bit to help engage the splines. If you're careful with the line-up, it should slide together relatively easily. Using longer bolts for initial installation to the engine can aid in aligning the units, but resist the temptation to use the bolts to pull it into place- it should slip together without excessive force.
Now bolt it up tight with the correct fasteners.