Catback exhaust - Stillen, Fast Intentions, Berk, AAM, one of the many JDM brands
Intake - Stillen or Injen
Manifold (exhaust?) - Fast Intention long tube headers (if removal of cats are ok with your location), if you need cats then Berk/Stillen/Fast Intentions for high flow cats
Brakes - Not sure of currently
Pulleys - NonStop Tuning or Stillen, would also look at an upgrade belt (gates belt I believe)
Short shifter - B&M and AMS
Beyond that there are not many more parts for an NA car currently unless you want to do other upgrades (audio, interior, etc.).
For my experience or opinion:
~Stillen Gen III intake, top gains and very solid design
~B&M shifter, solid upgrade, removes any rubbery feel in the shifter
~I will soon have Berk exhaust & Fast Intention LTH with more updates.