115HP Electrical Problem

I have a 1990 115HP ETLD that has given me four years of problems. The biggest issue is it will reach 4000 rpm and then kick back to 3000 rpm. I can never seem to get it up to the 5600rpm it runs at normally.
At first I thought it was a fuel problem and did everything I could to correct it. But now I am convinced it is an electrical problem and here's why.
I decided to disconnect the plugs one at a time to see what happens. When plugs 1,2,4 were disconnected the motor will run up to 4000rpm and then drop back to 3000rpm. When cylinder 3 is disconnected, the motor runs at 4000rpm with no drop. Thinking it might be a coil problem, I switched #1 cylinder coil (which was brand new last year) with #3 but I had the same results.
I got out my manual to see how to test the CDI and what I have on my motor does not match the manual. I expected to see wires mounted to terminals and what I have is attached in a photo. I was not supposed to have a YMIS computer either and yet there is this black box between the cylinders at the back of the motor.
Could someone please tell me what these are and where and what to test next?
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I messed up one of the pictures. Try this one.
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[boats.net]

That black box is the CDI unit, need to test pulsor coils, charge coils and CDI output.

This black box is an epoxied sealed unit. How do I test the output of it?

[boats.net]

Output is the peak voltage to each coil between black/white wires and ground, should be 125 volts at cranking speed.