i am actually ddealing with the same problem right know, so here it goes

1. break down entire engine assembly and lay it out exactly in the oreder these parts come off
2.take crank to reputable shop to be inspected (and polished if the crank is still usable)
3.have the rod inspected for damage (warpage)
3.inspect piston and oil squirter for damage
4.take block to machine shop for inspection (have it honed if ok)
5.order new bearings from honda by the color codes on the side of the bearing
(this would be a good time to replace main bearings and piston rings as well)
6.at this point you should know whats good and what needs to be replaced (replace with oe parts for best results or high perf parts not cheap rebuild parts)
7.obtain a total engine gasket kit (pref honda)
8.as you reasemble its always a good idea to plastiguage all bearings, check ring gaps ect
9.make sure you use a petroleum based assembly lube
10.inspect oil pump and housing
11.i always recommend a new timing belt water pump and therm with all rebuilds (oem preferred unless you are building the motor)
12.reassemble use torque specs and sequences if you dont have them buy a haynes manual
13.new oil and filter refill all fluids
14.check check and recheck timimg before initial start up
15. a good way to prime the engine is to take the efi relay out and turn the motor over x amount of times until the oil pump primes itself and the bearings

this is not a how to, rather just a small idea of what you are getting into, if unsure about any of this please go to a shop, no disrespect intended

mike please comment on anything i left out as i was in a hurry to type this