High voltage warning

Would that cause the engine to run rough?

One possibility comes to my mind. Carefully inspect your ignition switch wiring, the shield grounds in particular. Each electronic module should have its own separate, shielded wire routed directly to an ignition switch on the instrument panel, with each wire’s braided shield terminated to ground at both ends- the module and the panel switch. Use the current installation manual as your reference. The manual calls out separate ignition switches, but the traditional combined ACS keyed switch is often used as well. If so, a surge suppressor diode must be installed on your starter solenoid. The important part is to ensure all connections are clean and secure, particularly the grounds.

Would that also cause the engine to run rough?

Scot if you’re referring to my post, yes it would. 

Scot,

I’ve been thinking through what might cause both an ignition problem and high voltage indication at the same time, but to get there you may have to think of the two problems independently. I would focus on the high voltage indication first, and then you may see how that problem affected the ignition. As RW pointed out, you most likely either have a voltage regulator problem, or the regulator is not well grounded. I suspect the latter because that opens more opportunities for it to affect the ignition system. The ignition system is independent of generator and voltage regulator, but they share a grounding system on the carbureted 912. 

If the regulator is grounded through the mounting bolt, check the resistance of that connection. If you suspect the VR is not well grounded, a separate ground wire with a ring terminal under the mounting bolt is a good idea. Some folks install this supplemental ground wire back to engine ground. Also, check the resistance of the part of the airframe the regulator is mounted to in reference to the engine ground, and from the airframe to the negative battery post, and engine to the battery negative post.  All ground points should be zero ohms, or at least very low resistance, between them. 

If you find a grounding problem, this may also solve your ignition problem. There are multiple ways this could happen - grounding is a funny thing that way. Consider for instance that you found that the airframe and engine were not at an equal ground potential (a resistance between the two). In this case one thing that would happen is that the shield around the ignition module switch wiring (that Jim described), may end up carrying a voltage between the airframe and engine ground. This is possible because one end of the shield is grounded to the airframe and the other to the engine, and the shield would try to balance the two ground potentials. I could see that causing ignition problems.  

I’m not suggesting I have an exact solution to the problem, that can’t be done remotely. What I’m suggesting is a method of troubleshooting to get you on the right path, and that the two issues may be related in a way that will reveal itself during the process.