Hello Josho, and welcome to NSR-WORLD.
The MC16 does indeed have two CDIs under the rear cowl. They are prone to corrosion and "dry" solder joints, and it's not unheard of for one CDI to fail and the other to work, so try swapping them, and seeing if the spark shifts cylinders.
I wouldn't run the coils without spark plugs, especially given that they can be a bit fragile at 28 years old! Make sure you use the correct spark plugs too; B9ECS.
Although the CDIs can be a bit weak on the MC16, and the spark "look" weak on all NSR250s when the plugs are just grounded and the kickstart operated, you're really fighting against age and exposure to the elements. The last MC16 I had to cut into was so badly corroded, it was virtually impossible to solder joints, as the copper cores were black!
There are some posts here somewhere about MC16 electronics, but you will have to search for them, unless someone else can remember the author. I seem to recall he was able to adapt alternative CDIs from another Honda of the same period, that are more readily available.
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Andy.
NSR-WORLD.COM
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