Assume your pickups under the flywheel are similar to lower HP engines: One set of coils for triggers, another for generating voltage to charge the capacitors in your CDModule or CD system, and a third set for battery charging, all independent, non related (other than having insulation melt on the interconnecting wires and a short circuit resulting....you did say your rect/reg burned up.......) circuits.
Output voltage of rectifier/regulator depends on rpm and load current. A 16 amp red stator on a smaller engine is rated 16 amps max at WOT, but the voltage won't be 14.5V. Conversely, when a good battery is nearing full charge and the rpms are at max, the current will be in the low single digits and the voltage will have risen to 14.5V....serv. man. number. As long as your running (over 1k rpms) and battery voltage exceeds the value you had with the engine off, your charging circuit is working.
The question is, what kind of load is it driving? First thing I'd do is have the battery "load" checked....load checking forces high current out of the battery while monitoring terminal voltage. When the battery has a dead cell or sulphated plates, it can't do things like put out 300 amperes with 11V across the terminals, the numbers I use for pass/fail on what looks to be a good, fully charged battery.
Another possibility is that the supply from the stator can't deliver adequate current to the rect/regl because the interconnecting connectors on the wires feeding the rect/regl, overheated and as a result are high resistance...discolored insulation over the connectors is the clue to that and as said earlier, wires from the stators need to be inspected for melting insulation and shorts.
These thoughts keep coming to me....my third edit: Another possibility is that the "varnish" coating/insulating the wires making up the pickup coils in the stator(s) may have overheated and allowed wires to short together. It only takes one such wire, making a complete loop of current to kill the stator output.
The physics of the "transformer" are such that each turn has a given voltage it maintains and if that voltage doesn't develop, all the energy generated with in the device is applied to that loop, trying to establish the Volt/turn rating of the device. Hard to check with an Ohm meter as the manual's posted testing resistance for stators is fractional ohms.....but the two AC feed wires are to be insulated from chassis ground which can be easily Ohmed out.
. No problem while having some days fishing trip. By the way, I writing from Finland and like to thank you folks about help. This is really good forum!