Diesel Bombers - Rebuild advice?

I got a brother in law deal on a '99 F250 w/ 212k miles. The body and tranny is in great condition, but it had a dead miss and excessive smoke. Everything electrical checked out and the injectors were fine, but I did find four bad valves. I tore it down and did a head job and now I notice scarring in all of the cylinders. I've got so little invested in it that I'd like to go ahead and rebuild the entire engine while it's down. Any advice on what to do?

I'm not looking to hot rod it, I just want to do it right while I've got it torn down. I know the cylinders will need to be bored and I assume oversize pistons. The engine is currently 100% stock except for the exhaust. I'm mostly in need of advice on what to do to rebuild this engine to get many years of good reliable and dependable service out of it. Of course better towing performance for slightly more money would also be a viable option as long as it don't break the bank.