Are you still running the 6-volt system? If so, it will be very prone to having a low charge rate if any connections between the generator and the battery are loose or dirty. We used to run a test called a "series resistance check" that involved attaching a low-reading voltmeter from the Armature terminal of the generator to the positive post of the battery (the actual post, not the cable clamp). Any voltage shown on the meter during charging was what was being lost between the generator and the battery due to overcoming the resistance of the connections.
If there is more than 1/2 volt of series loss, for instance 7.0 volts at the generator and 6.5 volts at the battery post, start checking each connection for looseness or corrosion. The Armature and Battery connections at the regulator, both connectors at the ammeter, and the connection where the positive battery cable attaches at the starter are all possible high-resistance connection points. Of course, the most common high resistance connection will be the battery cable clamp itself. Then, do the same test on the ground side, going from the negative battery post back to the generator housing.
It's possible the voltage regulator is interpreting a high-resistance connection as a fully-charged battery, and cutting back on the output of the generator prematurely. I spent 13 years maintaining a 6-volt starting/charging system on a 47 Mercury with an 11:1 compression engine. Everything had to be perfectly maintained, with a high-current battery, before that one would start!
Jerry
