What do you mean by "homemade" Capac meter? The most important part of the Capac system is the electrode plate fastened to the hull. This is a silver compound that forms a battery with the water, giving about a volt between electrode and water. If a volt is measured between electrode and hull, then there should be no voltage between hull and water.
The electrode must be right or the readings make no sense. The meter itself is just a regular voltmeter with a pushbutton: current only flows (using up the silver stuff) when you push the button.
An electronic meter with high input impedance will not draw current and so the button is not needed. Modern Capac systems read all the time.
You can replace the factory meter with a digital one with 100Mohm or more impedance if you wish. I will spec one if you are interested.
The location of the corrosion makes me suspicious that shaft or rudder isolation may be a problem.
To check the shaft/rudder isolation from the hull when out of the water, you can use an ohmmeter between shaft and hull. Anything less than a megohm is suspicious. If there is a short, look carefully at the cutless bearing, the stuffing box, and the isolator at the transmission output flange.
The same check is done in the water by simply shorting the shaft to the hull. You should see a change on the Capac meter. If you do not, then the shaft is likely already shorted to the hull.
If you have an isolation transformer, rather than the little ground box, then there is no need to disconnect shore power for corrosion control. You can verify that it is wired correctly and working by measuring with an ohmmeter from the green ground on your dock plug to the hull. I have seen two where the dock ground was wired through to the boat's hull ground!
It is normal for the engine to be in contact with the hull. You should have a heavy yellow wire from the battery negative to a stud on the starter motor, and a smaller green wire from the stud to the hull. The engine circuits return to the engine block, and all others should return to the stud on the starter.
Marinette makes this work by isolating the transmission output flange from the shaft. Thus, the shaft, prop, and shaft zinc form their own private battery, leaving the hull alone.
Sorry to be so long-winded: Liz says I should have been a Russian novelist. This is a big topic and I don't know that much about it but I am sure that other members will weigh in.....
1975 32' Flybridge Sedan, twin Perkins 6-354 diesels, 1:1.53 velvetdrives, 16 X 19 props. Merritt Island, Florida