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I had problems using the alternator foot for grounding. The problem was identified when I checked the voltage between the block and the alternator case with the alternator charging. I added a separate ground wire from the case to the block. You may not need it, but check.
Most alternators (the Motorola included) are meant for automotive use. Their regulators (internal or attached) have a control voltage that I find to be too low for effective battery charging.
The alternator itself is not a complex device. The windings that make the power are located in the case, don't rotate, and have their AC output turned into DC by diodes pressed into the case. The rotor carries the field winding, which gets its current through two brushes and slip rings.
The regulator acts to control this field current. Two types of regulators: First is P type which controls the current going TO one brush, the other brush is grounded. Second is N type which controls the current coming FROM one brush, the other brush is attached to the alternator output. The alternator has to be wired to match the regulator and vice versa.
Second suggestion is to get rid of the A/B switch and use two separate battery banks, each controlled by a simple On/Off switch. The start battery (I found no need for anything larger than a Group 24) is connected to the starter and engine loads. House bank is connected to your distribution panel, and can be configured to your liking with more/less bigger/smaller batteries.
Batteries are charged from the alternator. The system that worked best for me was to send the alternator output to the house bank. When the house bank came up to voltage, a relay (VCR) would close and send current to the engine battery.
There are lots of ways to skin a cat. I've tried several, and this is what works for me. Hope it helps.
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