1996 50 hp Yamaha missing up to 2000 RPM

[kim1349.]

I have had this issue where this motor seems to miss on one cylinder until about 2000 to 2500 RPM at which time it kind of takes off and runs fine up to 5000 or 5300 RPM.
Here is what we have done or checked so far:
New non alcohol gas. Inline fuel filter remains clean and no water.
New correctly gapped plugs. Compression checked on each cylinder and good.
Plug wires good. Cleaned ground on CDI. No frayed or damaged wires. Set idle speed to spec. Rebuilt carbs. Seems to run fair in tank but has miss under load. Now trying to check or set syncronization but have this new issue. The commercial vacuum gage I am using fluctuates so fast and much that I don't know how to measure the vacuum to set the proper ratios. I suspect the problem all along is syncronization. What vacuum gauge must be used to dampen out the fluctuations? Does this represent a problem as the book makes it seem so straight forward. Any help is greatly appreciated!
Sparks

[99yam40]

if this is a 2 stroke motor you do not use vacuum to sync.

Just follow steps in manual for setting linkage and timing, then adjust pilot screws to spec and it should run fine.

Have you checked fuel pump for leaking into #3 crankcase

[kim1349.]

No this is a 4 stroke. My vacuum gauge fluctuates so rapidly and badly that I can not get a reading on any of the vacuum ports. Maybe there is a different vacuum gauge that's dampered I need?

All the carbs were rebuilt and it does not seem to lose pressure when you pump it up with the bulb. I doubt that's a leak from the fuel pump?

What's even weirder, we went and bought a different brand plugs because it seems that the plugs I got simply would not fire after being used a bit. I do have a spark tester and all show a good spark. Now when we pull a wire off the plugs one at a time, number 4 seems to do nothing. So is it the ignition module??

[99yam40]

Ok it is a 4 stroke,
needs a special expensive meter , vacuumate or something like that.
I am sure there are different manufactures for these gauges for outboard motors.

You can test inputs and outputs of CDI to see if all is in spec.
need special peak reading volt meter or a DVA adapter and regular meter

[kim1349.]

Ok. Understand about peak reading meter.
Can you give me the exact name for the vacuum meter needed? I searched for vacuumate and didn't fine anything relevant.
Thanks

[kim1349.]

Meter found

I did find it. It is a vacuummate 35-8111. Thanks