XJ650 ignition issues.

OK, so we're reviving an old XJ650 Maxim, and we have one coil that quit altogether. The only replacement we had available today was from an 85 Shadow 700. It seemed to work at first but the spark is at best weak and intermittent. I was only able to get two plug caps, and both new caps were on the problem outer cylinders. No matter what we do the outer two cylinders dig out under throttle.

Another strange thing is under mid throttle the rpms jump up and down a bit, very rhythmical, and I've never seen that?

I worry the issue could be the ignition unit, which, best as I recall can only be tested with a replacement unit. In that case, we have two Maxim 550s but afaik it's not interchangeable?

The guy working on it with me is sure it's just the coil.

Hoping some others have insights?

We've not taken a multi tester to anything yet but I have two more new plug caps on the way.

 

I’m surprised nobody has replied yet. Maybe they’re as perplexed as you. Hopefully you got it figured out by now.
I was thinking of the rhythmic idle. Was it running on all cylinders? A picture of a one lung engine popped into my head, because it would rev when the cylinder ignited and continue running but slow down little by little until it ignited again.
Or maybe a loose wire or ground that kept alternating connection with the vibration and exacerbating it.

 

most 4 cyl bike engines run a "wasted" spark system, you have a single coil with two plug wire outputs.
example.. cylinders 1 & 3 share a single spark pulse from the TCI/CDI, meaning when the spark unit sends a signal to fire cylinder 1, # 3 is sparking as well.

Many factors can cause your issue. from Cracked coil casing, weak / intermitent ground, broke down plug wire from coil, faulty resistor plug caps, cracked spark plugs, weak internal resistance of primary/secondary coils, corrosion on the ignition rotor, the condensor in the rotor housing, or for models with mechanical spark advance the mechanisims can have worn/corroded parts etc....

so you ask where does one start given all the possible causes? and my answer is start at the beginning of the spark signal... the pulse rotor on the side of the engine. this is the beginning of your signal. pulse rotor rotates with crank, energising a pulse signal to pickup, pickup sends this signal to CDI/TCI, as long as all safty sensors/switches let it pass (side stand switch/clutch switch etc..)

it then gives pulse signal to ignition coil/s, this "low" power signal enters the coil, coil magnifies this low signal to high output signal and thorough the plug wires, to the resistor cap (resistors are essentially one way electrical doors, and prevents this new higher power signal from returning to the CDI/TCI and blowing it)...... (if it fires and is not connected, it "can" travel back to CDI/TCI but not always)
and of course to the plug and bang!.... FIRE! (Actually electrical arc)

Each componet will have a set minimum and maximum value that can be tested. so get your bikes repair manual info for the specs required, and start testing from the rotor to the plug. pull ground wires off and remove any corosion to bare metal, apply some dielectrical grease and reattach. continue to test componets. there's members on here with your bike so they may have the specs you need.