A little information on the OEM ignition coils, it's highly unlikely that both would cause the same problem.
But if you have the gray and black coils, they are commonly referred to as the 'crack-o-matic' coil , they are a problematic part, and if they are not giving problems now, they will in the future.
BMW upgraded the coil some time in the early '90's, to a red and black part, I replaced my original gray and black coil with the upgraded part, and it only lasted 10 years before it failed again.
Just a little heads up info.
Have you replaced the fuel lines yet ?
I had a problem of one of the lines would kink on me and restrict fuel to the right carb.
Seeing as how you have a 'donor' bike, if you run out of places to go, you may want to try and swap the ignition canisters ( commonly referred to as the 'bean can') , located under the front cover of the engine.
If by chance the can is the problem area, there is a pictorial guide to taking the unit apart on our FAQ section, under the heading 'Bean Can Overhaul'.
Also there is an ignition control unit under the tank, it has an aluminum heat-sink bolted, or riveted to it, they usually work, or don't work, but it's a quick swap over.
From the looks of your profile, you appear to reside in saltwater coastal area, I don't know if corrosion is an issue with your area, but it would be a good idea to disassemble the electrical connections in the wiring harness, and check for corrosion and security of all of the connectors.
Welcome to the world of 28 year old motorcycles !!!!