'81 750 ltd carb questions

I've got an '81 750 ltd (four cylinder) with a 4-1 exhaust (no baffler, actually a cherry bomb on the end of th header... don't ask) with UNI Pod filters and aftermarket coils (can't recall the brand off te top of my head...). Dynojet stage 3 is installed

Bike starts pretty well. After a few seconds of running I start getting a small backfire through the carbs. It is random and is just enough to cause the engine to stumble for a second. That goes away after warm-up. I've already got my air/fuel screws turned out 3 turns. Should I drill the pilots?

Next...
The bike has a soft spot between 1800 and 3000 rpm, like it's getting too much fuel. I have been told the fuel level in the bowl will affect this rpm range. Does that sound right?

Next...
My Keihin carbs seem to have an extra jet in them. I'm used to the main and the pilot but there is a third one in there. Could that be affecting my popping and/or stumble? What rpm range does this jet contribute to?

Finally....
When jetting, do you start with the main or the pilot? I've heard it both ways, but what works on these bikes? It seems like my top end might be a little rich (cherry bomb is black on the inside) but I am tired of doing the dance without some knowledgable input

Thanks in advance

Jason

That soft spot is affected by the primary jet, that would be the third jet you speak of, should be a #62 if left stock. On my build, I left the pilot jets stock (#35)which affects 0 to 1/8 throttle, then bumped my primary jets to a #65 jet which will affect 1/8 to 1/4 throttle, and then shimmed my needles up equal to one notch which affects 1/4 to 3/4 throttle, and then bumped my secondary main jets up to #135, a little big, but better rich then lean, and this controls 3/4 to WOT. These all blend together in the throttle position, to help with smoothness durning acceration. I just got my bike running great couple days ago, plugs are a nice tan now and she accerates smoothly now, no dead spots anymore.But that's just my bike, every bike is different do to vaccumm in engine, but I'd just keep an eye on the plugs, I probably went through 5 sets of plugs and had taken out the carbs 8 times during my tuning process. But hopefully you can get it figured out.
Good Luck

where did you pick your primary jets up at?

Oh, really sorry for the very late reply. Site never sent me a message that you replied back.
But I pick my jet at www.jetsrus.com , you probably got a different place by now.
Sorry about that jason8887.