If anyone arrives here with the same problem on a Type II Thunderbolt ignition, I have finally figured this problem out. I found a boat salvage yard selling used parts and called them. I said that I needed ignition parts and ran the problem past the owner. He said that it sounded like a bad coil in my ignition driver and that he would just send me the entire distributor shaft assembly if they had one, I told him the number of my switchbox and told him to send one of those also if he had it. The parts arrived and I tested the old ignition driver and the new one. Here is how I tested them: white lead and red lead of the ignition driver measured 48-50+ volts AC while turning the key as a build-up reading on a digital volt meter (this is the wrong way to test it but gets you in the ballpark), blue and white read 10-20+volts, this was the same with both units. I ran the new ignition driver in my motor and I had the same problem as before, it ran for a few seconds and died with no spark detected immediately afterwards. I had a different switchbox also so I connected that in to the party. This is called swapnostics and it's the lowest form of mechanical problem solving there is but in this case it proved that the switchbox was the culprit. The motor was now making hellacious spark, the switchbox was loose from the frame and hanging by the wiring harness, I had one sparkplug out with a plugwire on it from an earlier spark test. The motor was running on 3 cylinders, I hit the kill switch/key, the switchbox was loose so the ground was intermittent, it wouldn't die, sparks were were jumping everywhere and I was happy again. I pulled a couple other plugwire boots and she died out.
Most of the older outboard mechanics I've talked to all have said that the symptoms I have explained did not sound like a switchbox issue, they said that switchboxes usually quit and stay quit. My problem was that I had 20 or so seconds of ignition and then it would be dead for awhile. I would get spark back after a few hours and then loose it again. As time went on the amount of time having spark would be less and less.
I hope this helps somebody out there someday.