There normally no over compression. It is just that normal compression makes a four stroke motor hard to pull start. A decompression mechanism momentarily prevents full compression when a starter rope is pulled.
Mercury Marine has approved a number of models for use with lithium batteries.
Although not approved by Yamaha, Suzuki, Honda or Evinrude, a number of owners of those brands are using lithium batteries with no ill effects.
CDI unit gets its input from the charge coil. It "charges" a capacitor within the CDI unit. The pulser coil tells the CDI unit when to discharge electrical power to the ignition coil.
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By signal I presume that the ground wire is not completing the circuit when it should?
And that the injector itself is known to be working?
Have you verified continuity on the ground wire from the injector to the ECU?