You might read over
this article by Mark Hamilton about remote voltage sensing. Although many cars run with the voltage sensing wire ran directly to the output on the alternator and yours ran that way previously you may want to change that. What is the voltage at the charging lug on the back of the alternator with the engine running? Compare that reading with the voltage at a main electrical junction and the battery. You might also check the voltage readings at a higher RPM to see how this affects the readings.
Just my .02.
Deron