What is the best and first mods you should do on the bike that provide the most performance and don't affect the reliability or warranty? Thanks!!

i don't have a 400 yet.

But, with what i've been reading. The best to do would be a pipe, rejet the carb, and do an air box mod.

Pipe(you have to rejet carb if you add a pipe), tires, aluminum airbox, rev kit, nerf bars, and so many more most other thing are gonna cost alot lot and aren't very nessecary if you aren't racing

First of all, check the throttle adjustment, almost all / if not all of the 2000 models are set wrong from the factory.

Rejet the carb, even if the rest of the bike is stock. Honda jetted them lean from the factory to keep the EPA off their back.

Run a higher viscosity oil such as 20w50. I prefer a synthetic myself (don't let someone give you the synthetic scare tactics, it's BS, Honda themselves even endorse synthetics in the owner's manual).

Although the stock suspension is great for stock suspension, the fronts are weak for my taste. They don't offer any adjustment other than preload either. On the same note, if you are jumping a lot, you would be wise to invest in a nice set of aluminum handlebars.

A lot of people are getting good results from exhaust systems (along with airbox mods), keep in mind all the aftermarket systems are pretty loud.

Listen to 86atc250r!! I just installed Dyna Jet kit,K&N airfilter,Outerwears,and modified stock exhaust.I will be getting aftermarket exhaust when I can figure out which one. Anyway the first thing I checked was throttle opening.It only opened about 75%.Adjust the cable so your throttle opens all the way and you will get some free horse power.

How do you modify your stock muffler? I've read that XR400 owner's cut out something on their baffle screen or something, but before the 400EX came out, one of the magazines said that this mod wouldn't work.

To modify your stock exhaust. Take off the end cap of your muffler.Grind off the three welds on the ring around the spark arrester screen,and remove screen,try not to damage screen.Cut the silent core center out of the cap( so that when you look into the end of the cap it's hollow), then clean up edges. Braze the screen back on to the remaining section of the end cap.Re-install cap.I got this mod off the net, from more than a couple people, and it's supposed perform as good as most aftermarket slip on's.

How much louder is it? Does it affect the spark arrestor?

It is louder than stock,but not as loud as some after market slip ons.This modification is supposed to be good for 2-3 hp.The screen is your spark arrester,as long as you don't damage the screen,and braze it back to the end cap it will be fine.When I did mine,I ended up cutting the top of the screen down by 1/2 in. then I brazed it in four spots back to the end cap. So now it looks almost like it did originally,except the quiet core is removed.Did you check your throttle opening? Mine was only maybe 70%.

How do you check your throttle opening?