OK dumb stupid move on my part I had the battery cables backwards on the battery. Explains everything other then why it was still cranking shouldn't it not crank if they are backwards. Next time I go to my parents ill have to check it out and see.
Well, you definitely blew the rectifier. And hard to say about the switch box. Might or might not be ok.
I suspect your root cause is a failed distributor trigger. Unfortunately the trigger housing itself is about $500 for a CDI replacement. Then you have to completely disassemble the distributor to replace the housing, along with installing new bearings.
Maybe your parts motor has a good distributor. You can check it by disconnecting the 3 wires from your existing distributor, then hooking up the parts distributor (obviously, that one has to be removed from the parts motor). Make sure the "test" distributor is grounded (with the normal dist ground wire, a hunk of wire, or whatever, to the block), and with the key "ON" turn the distributor shaft clockwise. You should get spark with a good distributor.
This guy on YouTube has the ign box test down pretty good, just jumper brown and white terminals as he describes. then momentarily ground the black terminal, and you should get spark out of the coil wire, if the switch box is good.
Anyway, there's enough info for you to test the critical parts of this ign system, the distributor and switchbox. I'd wouldn't worry about the coil, it's pretty tough and unless you see cracks in the laminations or anywhere else, it's very likely to be good.
I'll have to check that as well next time I go over to my parents. Is the rectifier what is connected to the stater if so good news there is its still good as I haven't connected it and have not hooked up my new stater yet.
I'll bring the extra distributor with me as well next time and test it. If not 500 dollars is still cheaper then a new motor. Just a matter of getting it all apart and back together and running which hopefully I can do. The engine did run though hopefully it was just a dumb moment for me.