Read some where to replace the lift pump and install a 2 micron fuel filter. What brands would you suggest? Also any other changes that need to be done to make my truck live a long and prosperous life. It's an auto that I rebuilt at 40,000 miles. Thanks

Clean fuel and clean air going into the engine are the key to making your Cummins survive. Don't use a cotton/gauze washable air filter, They let too much dirt in. Use the upgraded factory style 6 inch thick air filter for max filtration. For fuel filtering, I install 2 micron FF with water separator from Throttled-Up Industries, www.dieselfuelfilterkits.com They are a complete kit and with everything you need. They even include a tubing cutter to cut the factory fuel lines to install the kit. Mounts the filters nicely under the truck so they don't hang down too low to avoid possible damage. As far as the lift pump goes, I wouldn't worry about it much if the truck is stock or mildly modified. They are in-tank mounted, and are not as failure prone as earlier engine mounted pumps. FWIW, some of the aftermarket transfer pumps I have installed in the last year have had reliability issues. Specifically, the Chinese electric pump motors that some of them use. So installing an aftermarket pump may not be good if you are looking for reliability.

So I have just the filter attached to the side of engine, though that was the pump. Does the new filter bypass the original one? One other question I forgot to ask was about fuel mileage, my 92 got 19 to 23 mpg where as the 06 gets 16 to 19. Is there a way to get better mileage?

You can leave the factory fuel filter in place if you like. Wont hurt anything but it is designed to be bypassed. Your choice. The 06 wont get the fuel mileage that your first gen cummins did. By design it actually has 3 fueling events, A pilot, main, and after injection sequence. This is to make the engine quieter and also for emmisions. The earlier engine was basic with a mechanical rotary style injection pump that only fired the injectors once per cycle. They were easy on fuel but, louder and produced more emmisions.

There are a couple things you can do to increase economy. Some have had luck with Computer programmers and changing fuel injectors or nozzles to slightly uprate the power and improve mileage.

Thanks for replys, I think I'm going with the Cat filter system, looks nice.