I'm guessing you won't be running vtec. For one, the LS head flows like crap. I would pull the head and take it to a machine shop for a good port job, as well as a port-match on the manifold. Run a larger throttle body (65mm-70mm), and do a valve job.
As for the bottom end, you can do this the "cheap" way, or the "not so cheap" way.
Cheap way:
Take the oil pan, oil pickup and windage tray out. Now you can removed the rod caps and push the rods with the pistons on them out of the deck of the block(being that the head was removed already). Now mark each rod/rod cap for each cylinder so they go back in the correct order. Get pistons (low compression, 9:1cp works well) and have a machine shop press the pistons onto the LS rods and apply ARP rod bolts. Install new piston rings (OEM is fine). Pickup a set of Rod Bearing (ACL or OEM), apply lubrication to the bearings before installing and re-insert piston and rod assemblies back in the correct order. Torque down rod caps to ARP's Spec. Put the windage tray and oil pickup back on, bolt the oil pan back up with a new gasket, and replace the rear main crank seal.
Assemble engine, install and break in the rings on engine (no boost) with 5W-30 for 1000 miles. Change oil and go from there...
Expensive way:
Let the machine shop tear the block down completely, hot tank it, micropolish the crank, all new seals and bearings throughout, new pistons/rods, new oil/water pumps etc. (Costly)