Here are a whole list of positives and cons for modifications to your Honda engine while keeping it naturally aspirated or also known as All Motor mods.
Intake modifications:
Short Ram Intake: Less exposure to incoming airflow, more prone to engine bay heat in original form.
Cold Air Intake: More airflow exposure, cooler air intake charge, prone to water damage.
Throttle Bodies
Bypassing coolant lines to TB:
> coolant warms the incoming air
> coolant prevents TB butterfly from sticking in cold weather conditions
> The process is included in the installation directions when installing Hondata or other intake manifold gaskets
> longer engine warm-up time
>eliminates functionality of fast-idle thermo valve
Tapered throttle-bodies:
> taper helps increase incoming air velocity & helps keep some low-end
Individual/multiple throttle-bodies:
> increased throttle response
> air travels shorter distance
> less air friction than traditional intakes
> expensive pre-fabbed ITBs are available such as: Toda, etc.
> difficult to tune
Intake Manifold
Plenum - This is the air chamber which is found above the runners of the intake manifold. The plenum acts as a resorvoir of air, ready to be sucked in by each cylinder. Sometimes increasing the plenum volume helps with performance if your engine breathes well and other times it makes no difference because your engine is already maxed out on how much it can breathe in. So it really depends how it is tuned from the factory.
Runners -
Port-size: Each engine has an optimal runner port-size that gains the most volume at the least loss of air velocity. A taper in the runners can help balance air velocity with volume.
Length: Long runners make more torque/low-end and the shorter runners are for top-end.
Geometry: For best airflow, the runners should have smooth bends or keep them straight as in some ITB setups. Tapered runners can help balance air velocity and volume.
Finish: A semi-rough finish helps with fuel atomization and with power on the inside and cylinder head end of the runners.
Cylinder Head
Portmatch - Portmatching can be done on both intake manifolds and exhaust manifolds/headers. At the point where the manifolds meet the cylinder head ports, the mating areas are cleaned up so they flow well into each other. This aids in getting the most potential out of your existing setup.
Mild Port & Polish/Clean-up - This involves a portmatch, but also involves going into the ports to clean up any flash. No excessive porting is done rather a port clean-up. This will flow a better than a port-match, but still nothing too exciting.
Performance Port & Polish - This involves all the above plus usually enlarging the ports some, cleaning up the casting flaws, using certain grit rolls, etc. for good flow and A/F mixture. This job is usually involved with a valve-job, new valve stem seals, head cleaning and resurface and/or mill. They hit both intake and exhaust ports.
Camshafts
Naturally-Aspirated/Nitrous - Camshafts for NA based setups have more duration and more overlap for the effect to recharge the cylinders with a fresh intake of air.
Forced Induction (i.e. turbos & superchargers) - Camshafts for forced induction setups have less overlap because with a pressurized intake you would defeat the purpose of filling the cylinders to their max potential.
Valve Lift - This is the distance a valve opens from the closed position at the valve seat. Camshaft specifications are given with max valve lift measurements for both intake and exhaust.
Cam Lobe Lift - This is the distance from the outer diameter of the cam base circle to the tip of the tear-drop shape. Camshaft specifications are given with max cam lobe lift measurements for both intake and exhaust.
Rocker Ratio - This is the ratio number you get when you take max valve lift and divide it by max cam lobe lift. This ratio is handy if you retain your stock rocker arms on a performance build and use a performance camshaft(s) of some sort. Using this ratio, you can indirectly find the max valve lift for any camshaft(s) that you know the max cam lobe lift specifications for.
Overlap - Amount of duration (degrees) that the intake and exhaust valves are open at the same time. This is related to the effect and on most naturally-aspirated engines can produce more gains in power, some engines are more responsive than others. This can be used on forced induction setups as well.
Header
Off-shelf Header: Brands like X-Force, DC sports, Megan Racing, DC-S, OBX, etc. are the basic bolt-on modifications such as intake, exhaust, mild camshaft(s) with low compression ratio. Most of these are 4-2-1 design.
Kamikazee Header: These are different from the usual headers as they have 4-1 design and 2.5″ collector and same size down-pipe. This header will need to be port-matched to the head and replace the manifold-to-downpipe gasket with something of better quality.
Custom Header: Custom are only really needed for real extreme setups that already have had a reasonable amount of head work, exhaust and intake modifications done.
To advance or retard the ignition timing at the distributor housing: