Cylinder 3&4 fault

Working on a 912is with 39 hours, after the master switch was left on and running the batter dead we started getting a fault on cylinders 3&4. The two may not be related but interesting the problem started after.

Turn master on turn lanes A&B on light come on then go out, normal.

1. Start engine lane B light comes on and stays on, and G3X reports faults.

2. Used BUDS level 2 to troubleshoot, no clear issue found.

3. Two shops recommend replacing the ECU, did the swap, no change

4. Ran new harness from cylinders directly to ECU, no change.

I'm stumped