The majority of off-road motorcycles have poor overall chassis set-up. This is whether they are new or used, regardless of displacement/plastic color, or how cool and flashy the stickers are!  
     One major differences between a beginner's bike and a factory rider's bike is the knowledge of the person who wrenches on it.

So as far as chassis set-up goes, having proper spring rates, race sag,
head bearing tension, rim clean, and freshly bled forks, is the absolutely the FIRST STEP
in getting your bike to handle better.
ALL of these MUST be done prior to any suspension adjustments! Here is how !

Setting Sag

    There are a lot of handling problems associated with incorrect chassis set-up.
The most common problem is incorrect race sag/free sag.
The proper amount of race sag for a full sized Japanese motocross bike is 98-105mm.
The proper amount of free sag is 25-38mm.
Contrary to popular belief, a 2mm difference in race sag can make a dramatic difference
in overall handling!
KTM  (non linkage models) can run as low as 115mm race/40mm free sag

Step 1: Put bike on a stand with both wheels off the ground.

Step 2: Take a tape measure and measure the FULLY EXTENDED length of the rear suspension. This is done easiest by measuring from the rear axle to a spot on the rear fender,
THAT IS DIRECTLY ABOVE THE AXLE... This R1 Measurement !
I usually put a small piece of tape on the fender and leave it there as a consistent reference point. DO NOT MEASURE FROM THE REAR AXLE TO THE SEAT BOLT, AS THIS USUALLY ISN'T EXACTLY VERTICAL. Like I said earlier, 2mm is a very big deal.
WRITE DOWN THIS MEASUREMENT!

Step 3: Put on all of your riding gear that you would normally race with.
Take the bike off the stand.
Have someone stand in front of the bike, holding it upright.
Sit on the bike in the normal riding position, with your feet on the pegs.

Step 4: Have a friend pull down slightly on the rear of the bike, then SLOWLY let it come back up on its own.
Measure the exact distance between the same reference points.  This is R2.
WRITE DOWN THIS MEASUREMENT! 

Step 5: Now have a friend lift up slightly on the rear of the bike, SLOWLY letting it settle.
Measure between the reference points again.
WRITE THIS MEASUREMENT DOWN!
The average of these two measurements is the TRUE RACE SAG.
If the two measurements are more than 5mm different, the rear suspension linkage assembly is sticking and must be serviced. 
If the race sag isn't between the 98-105mm range, it can be adjusted by tightening or loosening the shock spring preload with the spring's retainers.

Step 6: Stand beside the bike and hold the the bike straight up by the end of the handlebar.
Have a friend slightly compress the rear suspension, then SLOWLY let it extend on its own. Measure between your reference points.
WRITE DOWN THIS MEASUREMENT!

Step 7: Now slightly pull up on the rear of the bike, then SLOWLY let the rear end settle under its own weight. Once again, WRITE DOWN THIS MEASUREMENT!
The average of these two numbers is the TRUE FREE SAG.
As with the race sag, if the two numbers are any more than 5mm different, your linkage is sticky.
If the free sag isn't between 25-38mm, WITH THE CORRECT RACE SAG,
you will need a different rear spring rate. If there isn't enough free sag, your spring is too soft.
If there is too much free sag, your spring is too stiff.

IF YOU DO NOT CHECK YOUR SAG USING THIS  METHOD, YOUR SAG WILL BE INCORRECT.
THIS IS ABSOLUTELY THE BEST, MOST ACCURATE WAY TO DO IT, HANDS DOWN!

www.racetech.com is an EXTREMELY GOOD website, and it  has a spring rate search.
This is the only website that I have found with an accurate one.
Every spring rate that RaceTech recommended that I install, had the EXACTLY perfect amount of free sag vs. race sag. TRULY GOOD STUFF!
   
     Tire Pressures

90% of riders do not set their tire pressures properly! The majority of riders just set their pressures somewhere between 12-15 psi, and never really give it much thought.     
The majority of riders have absolutely no idea what tire pressure they should run, so they usually ask their buddy, who probably has even less of a clue as to the reasons why he runs what pressure! Especially if he's stubborn and says he's run 38psi for 50 years,  and it always worked good...

     There is only ONE METHOD to deciding the proper tire pressure. Its called RIM CLEAN... 
There must be up to, a max of 4mm of a clean strip to the outside of the rim where it contacts the tire. The tire rolls over the rim somewhat, keeping this part of the rim clean!
ALL off-road motorcycle tires are DESIGNED to work this way! Front and rear.
"D" shaped rims will require less rim clean for obvious reasons.

     The tire pressure is adjusted so that the proper amount of rim clean is visible. 
The tire pressure can differ DRAMATICALLY from tire to tire, tube to tube,
bike to bike, track to track!

    A soft carcass tire with a stock tube may require 16 psi in order to have the proper rim clean.
A hard carcass tire with a heavy duty tube, may only require 9psi! 
So if you have a stiff tire with a stiff tube, and you have 15psi of pressure,
it may be the equivalent to running 20psi!

    It is very easy to run the wrong pressure, but most people don't know how to calibrate it.
If you have the proper amount of rim clean, and your buddy has the exact same
bike/tires/tubes but he has no rim clean, you theoretically may have 10% MORE TRACTION.
Now that's a big deal.
     Tire pressure (psi) is only a number, and that number is used to calibrate the rim clean..

     Steering head bearing tension

is also another thing that is often overlooked.
      Place the bike on the stand, with BOTH wheels the same distance off the ground. 
Slowly turn the bars from side to side.
There must NOT be any "crunchy" feeling spots throughout the sweep.
If there is, the head bearings are roasted, and must be replaced.

     With the proper amount of bearing tension (and a well serviced bearing set),
the wheel will stay 1"-2" OFF OF CENTER BEFORE IT FALLS TO THE STOP. 
If the wheel won't stay centered on its own, the bearings are too loose.
If the wheel stays more than 2" off of center, without falling to the stop,
the head bearings are too tight.

     This is a general guideline. Most riders prefer it this way. There is absolutely no bad handling traits associated with the head bearing tension, if they are set using this procedure.

     Slightly loose bearings tend to make the bike want to head-shake more while braking hard,
and it makes the bike feel sloppy. Slightly tight bearings tend to make the steering darty, especially on the face of a jump.
 Both increase arm-pump.

     Bleeding the air out of your forks.
Most riders aren't aware of the fact that your forks need to have the excess air bled from them. 1/2 the riders that are aware of it don't do it properly.  NOTE AIRFORK Models requires pressures to be set on a weekly basis !

     Put your bike on the stand, so that at least the front wheel is off the ground.
Take a small screwdriver, and crack the bleeder screw loose from the top of each fork leg.
DO NOT try and turn the damping adjuster, the bleeder screw is located to the side of the fork cap, NOT in the center.
Leave this screw loose for a few seconds, until you can't hear any air hissing out, then re-install it.
DO NOT DO THIS WITHOUT THE BIKE BEING ON THE STAND! (front wheel off the ground).

     It is best to do this before and after EVERY RIDE, as it will make the fork's performance
a lot more consistent, and it will lessen the chance of a blown fork seal.

     If your bike is going to be tied-down in the back of a truck or trailer, for an extended period of time, It is also a great idea to bleed the forks when they are compressed. This will take the pressure off of the fork seals. Just remember to re-bleed them as soon as you un-tie the bike!!

    
     NOTE: A lot of riders just ride their bike, and never adjust anything.
In a lot of ways, that is perfectly fine.
Most riders only do the bare minimum required maintenance on their bikes.
Everything listed here is just a good recommendation.
Having a properly set-up bike won't necessarily decrease the bike's lap-times, on it's own.
But, having as many mechanical advantages as possible, will lessen the chances of
INCREASING your lap-times unknowingly.