Sounds lean but looks like its running rich

So this is my first motorcycle and I'm at a loss:

I have an '82 750 Spectre w/ Kerker exhaust (I had just repacked the muffler) and a K&N replacement filter (I think it is completely stock other than that). I sent the bike to a shop to have the CV34's rebuilt and a few other things done. I got the bike back and it ran great, for the most part. It had a little hiccup at 3900-4000 RPMs. However, rolling a bit more throttle on and it would smooth out. After about 40 miles of riding, that hiccup started to grow. The point I took it back to them, I had ridden it about 110 miles and its hiccup grew to a nuissance. Now it would stumble from about 2500 - 4500 but above that its fine. They thought it was running lean; I think there is something else going on. I would think if it was running lean, it should have always run bad - this got worse. They tried the lean route, because it pops and gurgles like its lean (however, after riding you had to change your clothes b/c you smelled of exhaust - like it was rich). They shimmed the jet needles, took it out for a ride and it got worse. Pulled the plugs afterwards and they were black. That's the last I've heard

Now, since the end of April, they have had it twice for a total of about 8 weeks. I'm getting fed up and about to go pick it up. The question I have is, where do I start? Is there a common cause to make a bike do that? What jets should be in the carbs for a bike with those mods? Any other thoughts?

Thanks for your help!

I should also make mention, I haven't ruled out ignition. The module that's on the bike is a Kawi piece, but not the stock one. The mounting hole pattern is spread too far apart for it to mount in the correct location.

Let's start with something simple: Go to the nearest auto parts store and buy either one of these ignition testers:

www.lislecorp.com/divisions/products/?pr...ivision=1&category=8
www.lislecorp.com/divisions/products/?pr...ivision=1&category=8

They will help to determine if the spark is weak. How's the compression? Valves been checked for proper clearances? Tried another brand of sparkplug with the same problem?

Don't remember the exact numbers, but compression was good. Not sure about the valve clearance. Pretty sure the plugs I've got in it are NGK BR7ES's.