The drill bit and screw have been addressed. They don't apply in your case. Your jet needle pictured is from DJ. DJ needles in your kit have 6 e-clip grooves. Factory jet needles have only 5.
As for properly jetting with the stage 3 DJ kit, with a quality pipe like V&H or Kerker, and quality pods like K&N...Use the 138 DJ mains, place the jet needle e-clip in the 3rd groove from the top, if this results in a little too lean then place the e-clip in the 4th groove from the top and then place the DJ provided jetting spacer directly on top of the e-clip. The thicker spacer (ring) goes on top the e-clip or jetting spacer if used and the thinner spacer goes under the e-clip. That adjustment is equal to "position 3 1/2". I seriously doubt you would need to go richer. Set the float height to .95 which is in the middle of the factory setting range of .90 to .98". Be very careful adjusting them. Be sure all of the float needle valves are in good condition and DO NOT mix the valves with valve seats as the valve and seat wear as a unit. Mixing will result in fuel leaking through. Also be sure to replace the fiber gasket for the seats. The stock pilot jets (15) are fine as is. Initially set the side air screws at 2 turns out from lightly seated. Initially set the pilot fuel screws underneath to 1 1/2 turns out from lightly seated. REMOVE the 2 float bowl vent lines to allow the bowls to vent better. Do not cap the vents. Leaving the vent lines on will result in various levels of fuel starvation, especially on windy/crosswind conditions. Carefully bench synch the throttle valves. Unless you're extremely lucky, the bench synch must be followed by a vacuum tool synch with a quality gauge such as a CarbTune. Synch at 1,600 to 2,000 rpm's by setting the idle adjuster knob. Once synched properly, fine tune the side air screws using the "highest rpm method". Place the bike on the center stand is best. With the air screws initially set at 2 turns out, be sure, as with the synch, to warm the motor fully, place a fan or two to cool the motor, set the idle with the idle adjustment knob underneath to ideally 1,000 rpm's. Start at carb #1. Slowly adjust the air screw in or out and listen for the highest/best idle. Once you find the sweet spot, stop. Re-set the idle to 1,000 rpm's by using the idle adjuster knob if necessary. Repeat to each carbs. ALL basic tuning must be done before synching the carbs. Valve clearances, ignition timing, no intake leaks, proper 5/16" fuel line, proper spark plugs and gapped properly, everything must be right before tuning the carbs and re-jetting.
Be very careful to not over-oil the K&N's. If you follow the directions on the K&N spray can you can easily over-oil them. "Spray each pleat" results in too much oil and the motor will bog when you open her up. Spray about "3 pleats at a time from 4-6" away with a fairly quick sweep of the can.
The real benefit of the stage 3 kit is in the more sharply tapered jet needles. You spend the most time riding at the throttle positions of 1/5 to 3/4 throttle. The jet needle controls fuel flow at those throttle positions with a small overlap from the pilot circuits and main jet. Besides the looks and sound of a quality 4 into 1 pipe and K&N pods, the HP gain is obvious compared to stock, but only at higher rpm's. At about 7,000 rpm's a properly jetted bike will pull away from a stock bike. If you don't really care about that higher rpm performance, then maybe going back to stock is best?
Keep in mind the stage 3 settings I suggest may require fine tuning of the pilot fuel screws and as I mentioned, changing the jet needle position. If you need to adjust the jet needles, you must always re-synch the throttle valves.
If you use the stage 3 mains but you use the factory jet needles, you'll most likely have to place the e-clips in the bottom groove (factory position is #3). The factory jet needles DO NOT mix as well as the DJ needles and often give poor results with intake/exhaust mod's, but not always.
If you go back to stock, the factory mains are #95. Jet needle position is #3 groove from the top on factory needles. Pilot fuel screws setting are impossible to re-set without emissions equipment. Try 3/4 to 1 turn out from lightly seated. Side air screws are as I said earlier. Put the float bowl vent lines on and route them to the sides and near the top of the stock air box. They need to be factory length or close to it. I forget now but about 18" long?
Any short cuts, such as not checking/replacing the intake manifold o-rings, not replacing the o-rings in the carbs, not doing the other tuning, will make a re-jetting inaccurate and frustrating.
Also, I have had bad luck with buying the genuine factory bowl gaskets lately. They are often harder than they should be due to sitting on a shelf too long? They can easily allow leaking. I tried the bowl gaskets from Z1 Enterprises and found that they are softer and seal better against leaks, at least for me. One other note, if you replace the manifold o-rings, replace the stock Phillips screws too. Use Allen screws instead. You can then torque them to about 9 ft/lb. First apply a light coat of high-temp grease to the o-rings to help them last. Be sure the manifolds are in good condition, inside and out.
I have never needed to change any other part of the jetting for basic intake/exhaust mod's, including larger pistons. The "air correctors" are not needed. Only with more extreme mod's would you maybe need to make changes to the air jets or throttle valve cut-away, etc.
Good luck!
