Well to answer your questions:
I installed a non emissions header from NWOR. You can keep the stock exhaust manifold, you just need to make block off plates for the hot gas lines that come off the manifold if equipped.
First off, my truck doesn't have A/C or cruise control, if yours does, you need to keep the vacuum lines and related switches that operate the idle up circuit when the A/C is on and same deal with the cruise.
Removed and made block off plates for the egr valve
Removed the charcoal canister( big black can below wiper motor) this created a nice spot for the arb compressor
Removed the dashpot ( valve thingy by the throttle linkage on throttle body)
Plugged fuel tank vent line the went to the charcoal canister and installed a vented fuel cap
steel vacuum line rail with all hoses. cleaned it up nice
Removed the vacuum switches on the valve cover. one was for the egr and one for the fuel pressure regulator
Ran a vacuum hose straight from the fuel pressure regulator to a vacuum port on the rear of the intake chamber
Plugged off unused vacuum ports
I also run a gutted cat which helps quite a bit on the upper end ( i keep a good cat for deq, it will not pass with out it
When its time for DEQ i install a good cat, put the dashpot back on( it helps with NOX) run it down to almost empty, dump a third a gal of denatured alcohol in the tank, put 3 gal of fresh 92 octane in and run her through the test. It also helps to change the oil too, if it wont pass.
Hope that helps and good luck! IMO its worth the work to simplify the engine