Early 99 or late 99? Easy to tell...is the "Powerstroke" badge on the door like the later trucks or on the fenders?
Cutting the muffler off is always a good idea. It lets the engine breathe and the turbo spool a little quicker. On the 'Stroke it's a little more difficult because the inlet and outlet are not directly in line. You can use a piece of flex-pipe to make the connection but it's not as sturdy as welding in a piece of rigid 3.5" pipe. Plus it makes the truck sound much better.
First things first, change all the fluids including the axles. Make sure the king pins, brakes, rotors, etc are all in working order. Replace the fluids with synthetic. Once the truck is capable or funning good, THEN you can start thinking about power additions.
The first cheapo power mod is the 10K mod. Do a search and you will find all you need to know about how to do this. There is another site that has a ton of tips on how to make the truck run a little better but I can't remember the address and it's not in my favorites.
Gauges are always a wise move especially for the auto trucks. And like I suggested in the other thread, check out
www.itpdiesel.com and ask Dennis to help you build your truck for what you're going to do with it.