Re: Mercury 90 EFI...No alternator
The charging system is stator driven AC Generator run thru a rectifier to convert to DC. Most EFI computers do not like the saw-tooth DC waveform as the voltage fluctuates too much, they much prefer a stable battery voltage as the battery 'cushions' that waveform to a smooth line.
You should double check to ensure the stator and rectifier are working correctly to charge the battery.
Use a volt meter and see what the battery voltage is with the engine OFF, then check again while running at 2500 RPM. You should see a rise in battery voltage at RPM.
I 'may' be possible to build a battery eliminator using a capacitor, or two, but I personally would not want to risk higher voltage damage to the ECU as the battery itself serves as a huge voltage 'cushion'. Excessive voltage will kill electronics.