I'm having a similar problem. I have posted about it and I have done everything suggested. I rebuilt the carbs, replaced all the vacuum hoses that were looking old or were hard. took about 15 feet! The fuel pressure is about 1.7 lbs. and flow is more than double the manual's spec. The auto shut off valve is working fine.
Mine doesn't exactly cut out and seems to be more related to throttle position under load. It will run up to about 6000 under half throttle. At about 3/4 throttle or more it bogs down.
My engine runs much worse with the air box removed. Obviously the vacuum in the air box is necessary to make the slides operate. It won't even rev properly on the centerstand without the air box fully in place and all hoses connected. If I had a way to do it I would try to open the slides manually at full throttle while riding in 4th or 5th gear. I have been thinking all along that this was caused by a vacuum problem but I have not found it.
This problem existed before I rebuilt the carbs but it got so bad it would not pull just off idle. It runs good now except at over 3/4 throttle regardless of the RPM.
I did discover that the clamps on the manifold boots would not tighten up. There is a spacer on the clamp bolt that prevents over tightening. I ground about 2mm off the spacers so the clamps would tighten. That helped it run better but didn't completely solve the problem. I'll be watching to see if anyone nails this gremlin.
thank God someone else has this problem, what you describe is EXACTLY what is happening to me!!!!! I was getting set to order rebuild kits, but will hold off for now. I assume that you have checked your timing belts as well?
pulled the top of the airbox and the filter, engine hit 6k on WOT!!! put air filter back on, and I get no more than 4750 again. lifting up the air filter a little bit at WOT while bogging down, the RPM's came up!!!!
This is a brand new air filter, so I'm pulling the carbs (again) to see if I can find a vacuum leak, my thinking is the resistance from the air filter is allowing air to leak somewhere between the filter and the intake.
Another thought and avenue to check would be a bad reed valve for the pulse air or air injection system. A bad valve would show up more on periods of higher back pressure in the exhaust putting positive pressure in the intake(s) I would not expect both sides to be bad. Positive pressure pulses I think would for sure screw up your slide operation. Rolling on the throttle easy very little back pressure, hit it hard and it should get a sudden burst of pressure backing up through the reeds.
The above problem would likely not show up as rich, lean or ignition related just runs like crap at times.
You should be able to see that with a manometer or the hose on floor of air box at right front. That hose should suck only and never have any air pressure out.
Reed valves and plumbing is pretty much hard wired into engine I think and not really easily gotten to, I do not know of an easy cheater way of checking except above or what is in the manual.
Double check that your air jet vacuum hoses on carbs are connected correctly. One carb is just the mirror reverse of the other, one mirror set of ports to one air jet controller and the other 2 to the other controller.
pulled the carbs to look over all the vacuum lines, noticed that there was a dark spot on the line going from the IASA check valve to the intake (hose number 11) under the rubber mat. closer inspection revealed it was a HOLE!!!!
must have gotten too aggressive with the pliers when I re-assembled it and pinched a hole in the hose. I'm not sure a small hole like that could make a difference, but I'm off to Autozone to try to find a suitable replacement and put it back together and let you all know!!!
After looking at the timing belt tutorial on this site last night, I didn't realize there was a timing mark on the crankshaft pulely closer to the engine, I had been lining it up from the mark on the end of the pulleys. When I lined up to the "inner" mark, I found I WAS 3 TEETH OFF ON BOTH SIDES!!!!!!
pulled apart the crankshaft pulley, found the last part of the pulley has a small teat on the back of it that goes into a groove in the end of the crank. Someone before me must have not lined it up when they bolted things back together.
Thankfully, I've been careful to rotate the engine several times with the spark plugs out to check before started it!!!!! I shudder to think about crashed valves!!!
I've put the crankshaft pulleys back together correctly now and corrected timing, I'll bet it runs a lot better when I put the plugs back in and fire it up!!
a quick ride after putting the plugs back in and checking carb sync gave good results, felt like it popped the front end off the ground when I hammered the throttle in 1st gear, definitely popped it off the ground when I hit second just south of the redline