clean as much of that gunk out of there as possible, its bad stuff.
the thing that goes from the manifold to the header is your EGR tube (emissions device). you can clean it (in fact, you should if its coated with carbon, but DO NOT MODIFY it. if you do, you'll mess up your EGR mixture which will throw everything out of wack.
you can clean and polish every part of your intake if you want. you probably wont want to attempt to increase the bore of the intake runners, but port matching the upper and lower intakes, along with the heads and exhaust manifold would be a good idea. the ideal outcome is a smooth path for the air to follow, with no casting lines, sharp corners, or rough edges to slow it down.
the cam probably comes out the front.
doing the work yourself not only saves you a ton of money, but it allows you to take pride in your truck, knowing you built it the way it is with your own hands. you know its done exactly how you wanted it done.