If you spun a bearing, think of all the metal that could have been thrown into the engine. A complete tear down and a trip to the machine shop is a must IMHO. Have the line bore checked, vat the block, pull the oil gallery plugs, run bore brush. Replace the oil cooler, it’s impossible to get all the metal out of it. One flake of bearing sitting somewhere in the oil pump, oil cooler and you've wasted a lot of money.
Yes, the pickup tube has a screen, but look at the size of the openings and the fact the oil filter goes into bypass mode when cold.
Rant off.

 

I have a 99 2500, 24v, 5spd. Started running like water in fuel. Slightly rough. No water in fuel. Ran rough at idle. Ok at speed 1500-2000rpm. Started out from stop & it started sounding like guy with sledgehammer in engine compartment. Local mech does gas only. He started it & says sounds like a rod. Can't get code from odometer. Reads mileage only. Have not pulled it to town (60 miles away) yet. Suggestions? Thanks. Mikeempire

 

I would pull the valve cover off first see if anything going on there pushrod-rocker bent or broke. This going on with one cylinder makes a lot of noise. It will make you think its coming apart. Have you adjusted the valves? Rods are not common these things are massive compared to other diesel engines. I would dig around a little before x-ing this engine out.
Cookieman

 

Have your local mechanic hook up his scanner and check for codes.