I have a 2000 400ex with the 440 big Bore kit. It runs really hot and lean so I know their is a jetting issue. It has a shorty pipe (not sure what kind bought it like that, it's short and red and has no marking) on it with a K&N air filter and I run it without the air box lid. Has a hard time starting and idling. It also cuts out (spits and sputters) if you hammer to half throttle or more. I pulled the carb apart and it has a 38 pilot in it and a 170 main. Where should I go from their??
Thanks
Oh almost forgot when I was trying to get to the carb I noticed the air inlet on the carb didn't have anything hooked up. The air hose or whatever it is called that comes from the airbox wasn't attached just laying there and didn't know if that made a difference

 

Make sure your air mixture is set to factory spec according to the manual. Your big bore and exhaust will have no impact on air mixture setting. Set that to spec and it should get you running. Afterward, see where you are running into issue.. 3/16-1/2 throttle-ish you are looking at pilot issues. If you have what they call a "hanging deceleration" where you rev it at it just doesnt seem to want to back down, up your pilot size.

Chances are your pilot is fine. I built a 440 about last year, and only had to change the main (though not sure what I ended up going with). It had a full white bros exhaust and K&N.

You can also check out Sigma jet kits on ebay... typically around 30 bucks or so, you tell them your setup, and they send you the jets you need, plus a few extra for adjustments.

As for that air inlet. Are you talking about the small air hose on the carb itself? Or the clear plastic snorkel that goes from the airbox under the gas tank? Pics?