first runup to 4000rpm on new 912ULS

For what its worth;

When trouble shooting/diagnosing, it is psychologically difficult not to leap from one (often expensive, usually more complex) solution to another. 

I do not claim to be perfect in this area but do to strive to start with the least costly, usually less complex, potential solution(s) and try against all my urges to just implement one at a time, in some sort of logical progression.

I had another ignition module and swapped B out. It made no difference . Still getting 1000 rpm drop and fouled plugs in cylinder 1 and 2.

Alan

But you used the same connector?. That is why I recommended swapping connectors, not modules.  The modules are factory tested prior to delivery. The ignition module connector wires are pinned by the customer or his/her mechanic after delivery.
Following up, when you checked ignition wire grounding, you have two separate shielded wires (not a twisted pair) and the wire shielding is grounded at both ends (the modules on the engine and at the cockpit switches) correct?

Was your engine affected by the most recent carburetor float SB? Please describe how you set the idle mechanically before pneumatic balance.

engine not affected by carb sb

idle set per Rotax manual

I'm thinking the coil that goes to cylinder 1&2 bottom plugs isn't working as turning A off results in losing these cylinders 

It could be, but if this is a new engine (meaning less than 12 months old?) the probability of a new component failure is close to naught.  The greatest likelihood is something that someone touched/modified/installed/adjusted after delivery.