1st and formost find a very good machine shop.
2nd Get a OEM Dodge service manual!
3rd Have the machine shop check cylinders for wear and order correct size pistons/rings/wrist pins from Cummins.
4th DO NOT turn the crank, it has a special harden process done to it.
5th Call Piers for one of his cams.
6th Have the rotating assembly balanced by the machine shop (well worth the money).
7th Almost forgot, if you have a "53" block, get a new block.
8th Do not cut corners on gaskets, stay with Cummins(NOTE front and rear main seals are installed DRY).
9th Replace Oil pump, and water pump,
10th have oil cooler checked for leaks and damaged.
IF you have the money and are going for Big HP , ARP bolts and studs, Head port job, O-ring the head (or order one of Piers ready to go heads).
Get fuel pressure and trans temp gauges installed. Flush trans lines and replace torque convertor with a billet unit.
Lastly replace ALL Hoses and fan belt, Have raditor checked or replace with high quality unit.
Keep in mind this is the short list and I have missed a few things, and YES I have rebuilt a 5. 9 Cummins.
Hope this helps
Kyle