First, fix the dowel pin. Second, any significant changes you make to the engine will require an upgrade to the transmission or clutch, particularly the auto.
As for exhaust systems, save your money. The most restrictive part of the exhaust is the turbo housing, unless you're over 350 horse at the rear wheels you won't need any changes downstream of the turbo.
Ditto the intake system / air filter (other than tossing the filter housing-to-fender boot).
Take a look around TST's web site
http://www.tstproducts.com/ They offer a variety of power products and gauges. The fuel plate is the only real engine change you need
http://www.tstproducts.com/index.asp?PageAction=VIEWPROD&ProdID=119 along with some gauges to properly monitor what you've just done.
You'll get a lot of opinions about a lot of products like Banks, but for waaaaay less money you get the expertise of a guy like Mark at TST - Cummins factory experience and all.
No, I have no connection to TST, I'm just a satisfied customer.
Randy