I would at least inspect the clutch fork retainer/pivot thingy mounted to the bellhousing. Had some come off before, so it's better to fix it now, if needed, so you don't have to go back later.
Alignment tools are iffy even when you're careful, so if your transmission won't go quite all the way in, be prepared to install the pedal-to-clutch linkage so you can release some of the pressure manually and let the trans slip the rest of the way in.
You already said you were going to re-surface the flywheel. That's a definite must-do, so you're good to go there.
How many miles on the engine? Any oil weeping out of the different orifices yet? If so, now would be the absolute best time (next to having the whole engine out that is) to change a rear main seal and inspect the oil gallery plugs and cam rear plug to make sure they're good and not leaking.
And as was mentioned recently in another clutch thread, use some Loctite on your flywheel bolts. Some of them go all the way through, some are blind holes. Either way, you don't want it leaking and you sure don't want them coming loose.
Not that they'd to that of course...
Have fun!
Paul