Problem 2:  I was very disappointed to discover that turning off the alternator makes the engine barely run, especially with any other electrical load, even with 2 batteries connected.   They are fresh healthy batteries.  The voltage drops from 14.2 to 11.5.  If running at less than 2300 RPM when the alternator is turned off the engine begins to surge or stops running all together (however, running on just one set of coils improves the problem.)  If running at higher RPM the engine will just sag a little.

The coils and injectors ought to run fine on 11.5 volts.  We ran my 20B off batteries at the dyno, and ran a whole session not realizing the charger wasn’t connected.  Look for high resistance somewhere in the power leads to the coils or injectors – too small a wire, bad connection etc;

FWIW,

Al