Could be the breather hole is gummed up. Next time it dies, open up the fuel cap. If you hear a "whoosh" or the bike starts running again normally then the breather tube is gummed up. As the tank drains it needs to have air to replace the gasoline that is used up. If the breather hole is covered or half gummed up it will not allow fuel to flow. You could try running around with the fuel cap loose to test but be carefull, don't fill the tank right up to test. If you drive around with a half a tank a gas for hours with no problems that that is most likely the case. Also see if your petcock is working correctly. You can do this the lazy way by driving around on the prime setting, just remember not to leave it on prime when parked. If it works perfectly fine for hours then probably the petcock needs rebuilding, it's not that hard if you would like to save some money doing it yourself. If you really want to test the petcock take the tank off the bike, and stick a bucket or funnel underneath to catch any fuel. Briefly put the petcock on prime, does it flow fuel? If so connect some vacuum line to the petcock and suck with the petcock on either "On" or "Reserve", fuel again should flow out. Since the bike is still flowing fuel with the RPM's fairly high on prime, I would wager either the breather hole is a little gummed or the diaphram in the petcock is tired or sticky. Both are relatively cheap fixes. In fact if the breather hole is a little gummed up all you need to do is poke it through with a coat hanger or other piece of wire to clear it out, cost: free.
As far as rebuilding the petcock, usually you can get aftermarket kits for around $30 or $40 bucks and about an hour of work including draining the fuel from your fuel tank temporarily. It's pretty easy to do if you want to save $100 in labour costs, they usually come with instructions or you can just look at a microfiche and just replace what's already in there. The bitch part is draining the tank of fuel. To solve that problem you can ride until the tank is as low as it will go then tilt the tank on its side which will allow you to take the petcock off but the little fuel in the tank won't reach as high as the fuel cap. Just make sure it stays there while you work on the petcock so it doesn't tip over and spill any fuel. If you don't want to rebuild you can buy a high quality pingel type petcock which will probably outlast the bike but they are a little pricey but on the flip side it's probably the last fuel petcock you'll buy, they come in standard sizes and usually involve an adapter plate.
http://www.pingelonline.com/powerflo.htmAlso 2000 rpm for idle is way too high, it's hard on the gears when you go from neutral to first gear, set it back to where it should be. If you have a fuel delivery problem adjusting the idle won't help your just putting extra stress on the tranny for no good reason. I have a B12 and my idle is 1200 rpm, since you either have a 250 or 400 my guess is it should be around 1500 rpm. It's good your putting on that aftermarket exhaust your losing out on alot of power without it on there. I don't understand why someone would install a jet kit without putting on an aftermarket exhaust, all your doing is making the bike super rich and LOSING power. Considering popping on an aftermarket exhaust is the easiest part of rejetting I just don't understand. That you can also do yourself if you like it's only two bolts that hold the exhaust on there, one clamp at the collector box and a bolt at the end can and thats it. Just put a coating of exhaust sealant where the mid pipe connects to the collector box and your good to go, it's like a 15 min job. If the pipe comes with a centre stand stop then it takes 20 mins.