I picked up a 2001 5.9 recently with a supposedly 60,000 miles. I tore it down to the crank and Pistons and took it to a machine shop for the bottom end. A little over $600 for:
New rings
New main, rod, and cam bearings
New rear main seal.
Hone bores
Polish the crank
Chemical clean the block
New freeze plugs
Assemble
I started to put it together this week. Project creep got me... Edelbrock heads, air gap intake, double roller, etc, etc.