I followed the guide lines from the professionals at Modernperformance.com. They have a great write up on their site which I am going to use for mine. Modern performance broke down modifications into steps. the steps are building blocks of each other, from a starting point to an ending point. For example: you would not want to run a 20 P.S.I. turbo setup on a stock motor, as modern performance has a turbo setup as the final step because supporting modifications are needed to handle the increased power/ strain on the engine.

Guidelines as written  by ModernPerformance.com

We provide this guideline so that you will get the most bang for your buck.

The stages do not have to be performed in order, however we have them arranged according to cost/performance effectiveness. 

Stage 1 -Replace restrictive stock intake with a high flowing intake (Iceman or Kirk)

Stage 2- Replace heavy, restrictive crankshaft pulley with lighter, smaller pulley (MPx, or Unorthodox pulley)

Stage 3- Have intake manifold processed by Extrude Hone.
(due to the DOHC responding very well to intake modification, we feel that the extrude hone process belongs at #3.)

Stage 4- Replace stock exhaust manifold with Kirk header for higher gas flow output

Stage 5- Install large bore TB for higher air flow into engine from intake.
(MPx Billet TB) and port match the intake manifold.

Stage 6- Install prothane motor mount inserts, rear bobble strut, install new spark plug wires and MSD computer.

Stage 7- Install rear muffler (Vibrant, Thermal, Borla exhaust)

                    Stage 8- Install Hahn Racecraft Stage 1 or Stage 2 Turbo System

Turbo System - Recommended Upgrade Stages: (for dohc/sohc 95-99 auto and manual)
If you plan on going right into a turbo setup, these are the recommended upgrades/modifications.

Stage 1 - Hahn Racecraft Stage 1 or Stage 2 Turbo System

Stage 2 - Extrude Hone intake manifold

Stage 3 - 3 Inch MPx Exhaust- (or Vibrant, Thermal, Borla exhaust or custom universal.)

Stage 4 - underdrive pulley (MPx, or Unorthodox pulley)

Stage 5 - larger tb to match intake manifold (MPx Billet TB)

Stage 6 - rods and pistons to reinforce engine (Crower and JE )

Stage 7 - Prothane engine mounts (for the manuals- rear bobble strut upgrade)

Stage 8 - change spark plugs to non platinum plugs and use magnecor spark plug wires to withstand higher temps under hood.

Other options for either Engine equipped Neon's- Remove any material, seating that isn't necessary such as rear seats, passenger seat, any unnecessary stereo equipment, sound deadener etc