So stock header or aftermarket full system? If you have raised the compression ratio, then yes some of the full systems can be beneficial but if you are still at the stock ratio then the stock unit is more than adequate IMHO.
The way I look at it is that it is a fairly well designed system, built on the cheap. It is stainless but does discolor quickly, as we all know and the welds are a bit ugly and cause some issues but we'll cover that in a sec.
There is one "controversial" bit which is normally referred to as the "restriction" if you look into the header where the right mid-pipe mounts.
I say controversial because I have heard many times that Honda just left it in there to cut costs, which I don't agree with.
The reason I say this is by looking at the header you can see that the pipe extends 25-30mm past where the weld is located. Let's call it 25mm to make it easy.
If it is just to have a bit extra tube to make assembly easier, then 5mm would have been fine and it wouldn't extend into the collector, so no blockage.
Now 20mm of stainless tubing doesn't sound like much but factor in the production run and spares made and let's say Honda made 100,000 headers.
That 20mm now turns into 2 Kilometers of wasted tubing. How is that saving $$?
Another thing is they all seem to be in the same location.
If it was just sloppy workmanship then you would think they would be at different spots in the collector but that doesn't seem to be the case.
That leaves the question, why the hell is it there? After doing a bit of research and seeing Dan Kyle's dyno charts showing the bike made 2 hp more with it in (of course that was a week after I removed mine.....
)back in '97 I finally think I figured out what is going on. I could be wrong but the big clue for me is how the left (shifter side) can gets hot at idle and low RPM while the right stays cool and then heats up as you bring the rev's up.
What I believe they have done is tricked the exhaust gasses into thinking it is a variable length system, which is the best type of system to run as you have a long system for low rpm power and a short system for high RPM power. So how did they do this with no moving parts? Well exhaust gasses are stupid..... for example the 160 degree or so turn the rear pipe makes before it joins the collector make the gasses "think" the pipe is close to the same length as the front pipe.
As the gasses exit the "restriction" it wants to go in a straight line, so most of the flow exits the left side, or as long as the system can get.
As the RPMs raise, so does the pressure in the system which causes "the path of least resistance" for some of the gas flow to now be the right pipe. As more gasses start flowing through the right side, the system "appears" to now get shorter to the gasses flowing through the system. This continues until the flow is equal through both cans at which time the system "appears" to be at its shortest to the exhaust gasses.....at least that is how I see it.
Now after all that there is a place (well two places) where I have to say Honda did blow it. Yeah after talking about Honda workmanship I have to point out a big mistake IMHO and really points out the "made on the cheap" issue and can make me question my other opinions on the the system..... I mean how could you desigh something so good then screw up so bad??
Anyways the problem is on the inside of the pipe where it bolts to the head. Take a look down the pipe and you will see the biggest, sloppiest, nasty machine weld holding the collar on.
I don't have a pic of the "before" but on mine the weld stuck out 6-8mm in one spot and a good 3-4mm the rest of the way around. This is right where the exhaust exits the head...
I started with a die grinder with a stone to rough the weld down....yes the stuff is hard....lol then switched to a Dremel with a drum sander and then a 80 grit flapper wheel and you end up with this:
Not the best pic but it is hard to shoot down the pipe and get an image.
Also while on the exhaust, you should check it from time to time if you have dropped the forks, raised the rear or both as it is the first "hard part" to touch down though only in right hand turns.
What you will see if this happens will look like:
that was stupid of me, I obviously did not investigate fully enough. 
