As the mods that Gordon did get referred to almost constantly for an XR I've copied them here for posterity and stickied them.
The source was the XR400 Yahoo group.
So let's use this thread for discussion on these.
MY MODIFICATIONS TO A 2000 MODEL HONDA XR400R (Revised: Nov 25, 2000)
Stock Carb Specs
Main 142, Pilot #52, Needle Clip in 3rd groove. Right off the showroom floor, mine ran fine, but definitely on the rich side. Removing the airbox snorkel without re-jetting, however, made it run lean and overheat.
RELIEVING THE 2000 HONDA XR400R MUFFLER BAFFLE
(This is a very simple procedure, and one that can be almost as easily reversed. Best of all, though... it works.) After carefully examining the stock baffle/spark arrestor, and running some flow numbers for the different areas involved with the numerous plates and baffles (both in the muffler and on the baffle insert), I've come to the conclusion that the primary restriction to exhaust flow is the small final outlet, which has an i.d. (inner diameter) of only 20mm. Without removing the baffle insert from the muffler, examine the exhaust tip. Notice the actual outlet, which measures 20mm i.d. (approx. 0.787"). Around this is a larger 'bright finish' ring which appears to have no real function, but may be to help prevent the rider from coming into contact with the actual outlet, which probably runs hotter. Down in between the 20mm outlet and the bright-finish outer ring, there is room to drill 1/4" holes into the baffle to provide additional exhaust flow area. Holes drilled in this area will be 'inside' the spark arrestor screen, by the way, so the spark arrestor function is maintained. On my baffle insert, the area to be drilled is large enough to accept a 1/4" drill, but there's a benefit to using a #2 drill bit (0.21") (or maybe a 7/32" bit) which I'll explain a little later on. Since the stock 20mm (0.787") outlet provides a flow area of only 0.4862 sq.in., and a 0.21" hole has a flow area of 0.0346 sq. in., each 0.21' hole adds 7.1% more flow area. Just three such holes will increase the exhaust flow area by over 21%, and four will increase it by over 28%. First I ran the engine with the undrilled baffle, to get an up-close feel for the sound level at idle, and while revving the engine. After drilling one hole, I could barely hear any difference. After drilling a second hole, I could hear the difference, but it was slight. The third hole made a bigger difference, but still not objectionaably loud. The fourth hole made it just a little louder than I was willing to accept, adding a definite bark to the exhaust note. Since I had use a #2 drill bit, which is approx 0.21" in diameter (it's supposed to be 0.221"), I was able to plug the 4th hole very simply by screwing in a 1/4x28 set screw, which I woudn't be able to do had I drilled the holes with a 1/4" bit. This effectively reverted back to having just three holes, and it also indicates that I can plug them all with 1/4x28 set screws, to return to the stock sound level if necessary. Come to think of it, I guess you could say that this modification is "tunable" by inserting or removing set-screws from numerous holes. A brief test ride with stock jetting showed that the added three holes gave the bike a cleaner and stronger throttle response, probably because it runs rich when totally stock. It was now running cleaner, so the added 21.3% flow area was beneficial, and it had cost me nothing but a little time. It's also totally reversible by plugging the holes with set-screws. It is NOT necessary to remove the insert when drilling each hole. The metal chips will fall either outside the muffler, or into the screened area of the spark arrestor. Once you have drilled the desired number of holes, you can then remove the insert and shake out the tiny pieces if you so desire. If you don't, they will eventually fly out the exhaust outlet anyway, since the spark arrestor screen prevents them from falling down inside the main muffler.
GRINDING THE WELDED HEADER INLET
I'd read about the header inlets being partially shut off by the welding that builds up when welding the 1" i.d. header pipes to the clamping flanges, so I examined mine. Simply loosen the clamp bolt where the header pipes assembly slides into the muffler, and then loosen and remove the four nuts (two per pipe) where the headers are clamped to the head. The muffler bolt and all four clamp nuts accept a 12mm socket. Then the header pipes assembly slides forward and into your hands. On mine, a 2000 model, the built-up welded area in each pipe was terrible! The remaining opening measured a rough 0.75", leaving a flow area of only 0.44 sq.in. A 1" i.d. pipe has a flow area of 0.78 sq.in, so the welding left only 58% of that! I started grinding down the built-up welds using small grinding stones in my Dremel Moto-tool, but that was too slow. I went to the hardware store and bought some inexpensive coarse grinding stones to fit my 3/8" drill, and one 1" ball stone for finishing. I spent over two hours grinding away. As a "size guide", I chose an 18mm socket that has an outer diameter of 0.944" (different brands will vary in size, of course). Once the 18mm socket would slide into the header pipe, I quit, not wanting to remove too much of the weld, and weaken the joint. I then used the 1" ball grinding stone to finish up. Since the stone itself wears away faster than the weld material, I ground a little on each pipe, going back and forth between the two, until enough of the stone wore away to fit into the opening. This final touch didn't really make either opening larger, but it did make them both about the same size and shape. Since I started with a 0.75" opening, which had a flow area of only 0.44 sq.in., and finished with a 0.944" opening, which has a flow area of 0.670 sq.in., I achieved a gain of more than 52.5%. In one afternoon I significantly improved the flow characteristics of the stock exhaust system, and my total investment was under $10 (for some cheap grinding stones and one 1/4x28 set screw). I already had the 3/8" electric drill and #2 drill bit.
AIR INTAKE SYSTEM
I removed the air box snorkel, and then used a scrap of aluminum window screen to cover the opening to keep out trash and clumps of mud. I then removed the stock air filter and support, the latter of which includes the backfire screen. Noting that the backfire screen consists of two layers of screen, between which are trapped two more layers (actually a flattened screen 'tube'), I carefully cut away only the outer layer of screen, and removed the trapped inner piece, leaving only one, the inner layer, of the original four-layers of screen. I happen to like foam air filters, so I'm sticking with the stock filter for now. (I later bought a TwinAir filter, but with the backfire screen modified, I see no performance difference between the TwinAir and the stock air filter. If I were using a louder and more free-flowing exhaust, perhaps the TwinAir filter would make a difference.) NOTE: Cutting the metal screen is a chore, and it's difficult to get rid of every tiny little piece of wire (from the screen) you cut, so I no longer recommend cutting the stock backfire screen. Intsead, buy a UniFilter air filter for the XR400R. It comes with a screenless air filter support, and a less restrictive air filter. Despite what I read elsewhere, it is NOT necessary to move or remove the subframe to remove the carburetor! After removing the seat and gas tank, I simply loosened the two clamps holding the carb to the airbox duct and intake manifold, then loosened and removed the three bolts holding the intake manifold to the head. By turning the intake manifold a little CCW first, the carb and intake manifold then slide easily out the left side. After removing the carb from the intake manifold, I examined the composite rubber & plastic intake manifold. I do not think it was necessary, nor do I think I gained anything from it, but I used my Dremel Moto-tool with a medium size sanding drum to clean up the few ridges found inside. Just couldn't resist!
JETTING CHANGES REQUIRED
After two days of trial and error jetting (and a few hours more since then), I came to find that the exact same jetting recommended by CYCLE NEWS (several years ago) worked best. I'm using a 160 main jet, a #60 pilot jet, and the triple-tapered carb needle that comes standard in the 1998 and later XR400R's, with the needle clip in the stock (3rd groove) position. My altitude is approx 700' above sea level, and I ride regularly up to 3200', where it still seems to work just fine. I've also replaced the 15t drive sprocket with a 14t. For the terrain where I ride, the stock gearing is a bit too high. Depending on your particular machine, you might prefer a 158 main jet is using a stock or modified stock exhaust. If using a louder and nmore free flowing exhaust pipe, or the 1996-97 spark arrestor without the muffler insert, you'll want to use either a 160 or 162 main jet.
How my XR400R might compare to a differently modified version, I don't know. All I do know is that it easily pulls away from an unmodified 1999 model, and that I am able to pull up the front wheel at will in any of the first 3 gears. It is a little louder than stock, but not as loud as a KLX300 with its muffler tip removed, and it is nowhere near as loud as an XR or WR 400 with the muffler insert removed altogether. It's more than I need for woods riding, but without being 'difficult' to ride.
XR400R Spark Arrestor/Muffler Note
The 1996/97 XR400R has a two-piece exhaust pipe insert. The removable spark arrestor has a removable muffler insert. With the muffler insert in place, the exhaust is very quiet and very restricted. With the muffler insert removed, the spark arrestor alone has an open outlet nearly 1.5" in diameter, so it makes really good power, but is also pretty loud. The 1998/01 spark arrestor insert has the small 0.787" outlet which serves as the combined spark arrestor and muffler, all in one piece. It has more restriction than the 1996/97 spark arrestor alone, but more restriction than the 1996/97 spark arrestor with the muffler insert. Both of the two different spark arrestors fit all years of the XR400R's exhaust pipe (three small bolts).
Gordon Banks Huntsville, AL