A word to the wise. If you should happen to fry your ultimate coil, a new one will run you $100 plus shipping. A great coil I'm sure, but $100...must be a Harley part!!
Well, the 17-6903 "Ultimate Coil" is a high performance, very high voltage (82,000 Volts) coil. If you leave one of the spark plug wires disconnected, that voltage has to go somewhere, so it will most likely arc internally and create a carbon track, essentially shorting out the coil. That, and leaving the ignition on with the engine not running, is about the only way that you can damage the coil, and it is something that is completely under your control.
Proper installation of the coil is also important and there are a couple of recommended ways to install the coil described on the web site
www.yamahaxs650.com
The most common reason for disconnecting one spark plug is to perform the dead cylinder carb syncing method. If you have vacuum barbs, then you can instead just pull the vacuum hose or blind plug off of one carb at a time to kill the cylinder and leave the spark plugs connected.
If you do not have vacuum barbs, then you must connect the spark plug wire to a spare plug that is secured to the engine and will not fall off from the engine vibration.
We kinda got used to just pulling a plug wire whenever we felt like it with the original points system. The points coils only produce about 10,000 Volts and they are single output coils with an internal connection from the high voltage side to the primary, so there is a path for the high voltage to ground through the points. That's not the case with a dual output very high voltage coil.
Of course, if something were to happen to the "Ultimate Coil", you do not have to replace it with another "Ultimate Coil". There are any number of coils available that will work with the same setup as the "Ultimate Coil" for less money.
MikesXS sells a couple of them, including:
17-6822 37,000 Volts, long spark duration, built in plug wires, cool running 4.5 Ohm primary. $34.00
17-6810 75,000 Volts "Green Monster", cool running 3.5 Ohm primary. $69.00
Other vendors also carry suitable coils:
Custom Chrome, 17131 HD OEM 31609-80, 35,000 Volts, 2.8 Ohm primary, available at your local HD dealer, $39.99.
The 17-6822 and the HD 17131 are more tolerant of a disconnected plug wire and you can probably get away with one or two mistakes.
So, if you can get a good coil for less than $40 that's more tolerant of abuse, why not? Well, I have had all of these coils installed on either my '78/E or '81/H over the years, and they are all good coils. But, the "Ultimate" 17-6903 is the bomb. Instant starts, road tested higher gas mileage, overall smoother operation from idle to cruise. I have had the "Ultimate Coil" installed on my '81/H since last year to evaluate it for Mike and I'm very happy. I run an ultimate coil in my test rig that is used to test all of the PAMCO's prior to shipment, and that test rig includes an oscilloscope, so I can see the cleaner waveform and the longer initial spark duration.