yz400f driving me nuts, carb issues?

okay, I have a 98 yz400f, I bought it a couple of months ago solely because it had a CA plate, but it was in bad shape, I got a good price and figured it would be a great DS bike.

Anyway, did a full engine rebuild, bottom up, when I went to run it we started to have carb issues, first the hot start system, then just a pain on getting it right and finding the crazy jets. After a few times of messing with it I decided to get a newer style carb so I got a carb off a 426, it was in good shape, my mechanic installed the carb with the full JD jetting kit as per directions. It now starts relativly easy, and runs clean on the bottom and at the top, but at almost half throttle to say slightly above 3/4 throttle it cuts baddly. A couple of extra details, I have hotcams installed adn this bike came with alot of extra parts, it is running a wr stator, and I have an extra cdi box, I do not know which box is the WR box or the YZ box, or weather they are both yz boxes. Ideas? At this point I think I need to raise the needle, but I also want to know if I have a WR cdi as JD said that that also causes a studder in the ride. How do I know which CDI is witch?

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