If you are going to own that truck your list is good but are putting the cart before the horse. Make the truck reliable then worry about the intake, exhaust and tuner.
First you need to get to the root of the hard start, it could be the FICM if the truck has had any weak battery or charging systems problems. FICM's are not cheap and it is just as likely your injectors. Any shop with the proper diagnostic will be able to tell your if it is your FICM and/or Injectors.
Does the running rough get better as it warms up?
If you plug it in overnight does it runs smother from a cold start?
Do you have any codes, FICM, EGR or Injector related?
If any injectors codes are the contribution for a few injectors or circuit codes for all 8 injectors?
Answer those questions for me and I will tell you if it is injectors or FICM.
After you have detemined if it is injectors or FICM of both, you then need to deal with the EGR Cooler
... lots of options there.
Now your that your injectors are firing, your EGR Cooler is dealt with and your headgasket is at a much lower risk you can purchase a tuner (I recommend SCT
) then a high flow air filter replacement
, or cold air intake
if you want (not need) and finally an exhaust system
I see these things everyday and trust me, I really recommend taking care of the EGR system with the money you saved from throwing parts at your problem without testing...