The "optimal configuration" is bike specific, but we can get you close. I've posted the following before, but the search engine awaits tweaking, so I hope the inmates will pardon the repetition.
First of all, just for reference, your stock main jet should be a 142.5. I'm near sea level and run a 157.5 (open airbox, SXC muffler) most of the time. For our mountain/desert adventures, I drop in a 155 or so, depending on the season. A selection of sizes say from 150~ish to 165 will give ya plenty to work with to dial yours in. Stock up - they're cheap.
Getting at the main is easy on the '01 because there's plenty of clearance beneath the carb, so just remove the big nut on the bottom of the float bowl and there's your main jet right there. There'll be a little collar that comes off with it, so be careful not to lose that. I've done it a bunch of times with a stubby screwdriver, but using Motion Pro's main jet wrench makes it even easier. "8mm Round Part Number: 08-0024" as shown on http://www.motionpro.com/Docs/convtools_2.html
. After a few times, you should be able to swap a main jet out in a couple of minutes, start to finish.
The air jet is located in the carb's bellmouth, recessed into one of a couple of holes, with its screw slot facing the airbox. You'll wanna put a 1.1 in there. Here's an easy carb access tip: Remove the exhaust mount bolt just above the chain roller, along with the muffler's springs. Then loosen the clamp that secures the airbox to the carb and remove the subframe's upper mount bolts. Slowly pivot the subframe down towards the tire while watching to see which (if any) of the electrical connectors need to be unplugged to avoid pulling. The airbox will pop off the carb and you'll be able to remove it (the carb) with ease. Be VERY careful with the tiny air jet's threads and screwdriver slot.
Then just dial in the mixture screw like on most any other bike. Turns are counted outwards from lightly seated. Here's a handy guide...
Some relevant threads...
I believe in supporting your local shop, but here's a nice online resource for part numbers and schematics...
Specific to your carb...
Also, since the bike is new to you, here's a blurb about friendly gearing in case you ever feel the need: To keep your chain length the same and be able to easily swap street/dirt gearing as needed, go up one tooth in the front, and down two in the rear.
17t countershaft sprocket, ktm part # 58033029017.
40t rear sprocket, ktm part # 58310151040.
You'll need to take a belt sander to the removable case protector to fit the larger countershaft sprocket, or order up the one that they use on the duke (ktm part # 58430047000). Either way it's a no-brainer.
Soooooo, long story short, here's my typical setup and few part numbers...
17t countershaft sprocket, KTM part #58033029017.
40t rear sprocket. KTM part #58310151040.
KTM SXC muffler is part #58305081300.
Open airbox cover is part # 58406003200.
Main jet 157.5-ish, air jet 1.1.
Euro tool carrier thingy is KTM part #58012058000.
YMMV, and then some.