ignition problems hard starting

On the original alternator, one field terminal was grounded.
The 'two field' alternator and regulator differ as follows.
The blue wire still goes to the regulator - but only for the regulator to monitor system voltage.
It directly supplies power for the field -
Whether or not power flows through the field is controlled by the green wire whch completes the circuit to ground through the regulator.

A circuit with two isolated field terminals looks something like this.

Main_charging_wires_plus.png
For trouble shooting, I concur with TB's advice. But you might want t o make you're own circuit digram since you've modified the harness. It will help you see what a test means, and might make it more obvious what's wrong.