Logic and electricity

I'm not an electrician, not even close, but I can kinda sorta read a schematic some and know that wires, and switches and relays are very much like a computer program flow chart or a logic problem (both of which I studied in college about a 100 years ago and wasn't real good at but I do kind of understand the concept of "if A=>then B" and all that to some degree, and I did work in factory where sometimes I could logically convince the electrician where he should be looking to resolve the problem) so it really wasn't connecting with me as to why doing some static tests on a few component and removing a wire that wasn't going to be used would suddenly make the Honda not start at all.
But now I have a theory at least.
After we scrapped the idea of getting the electrical starter working (mechanical problem, not electrical) I decided to pull the wire, which was an add on and not part of the harness because of some previous owner's tinkering.
I took it loose at both ends, cut the visible ties and tried unsuccessfully to pull it out. Eventually the tank had to be pulled and more ties cut before it came free.
By now the battery is recharged and we want to start it to check some voltages while it's running to see if we can isolate the charging problem but it won't start. Not getting any fire, and not making any sense. Nothing we did should have made a difference, and it was starting so readily two days before.
When I initially reported that the battery wasn't charging some suggested looking for loose wires. A while later, since I seemingly wasn't getting any juice from the coil, I'm looking for some test for the coil. Find one, and the first step is to take the black/white wires loose from the coils to do a test...one of them is already kind of loose in the connector.  Ah-hah, maybe that is the charging problem, but it never came to the point of finding that out because the testing indicated that there was a problem with the spark plug caps and now I wait for those...
But this morning I get a revelation...the loose wire wasn't the charging problem but maybe it was the starting problem.  Looking at the diagram I find that the black/white wire at the coil comes from the run/kill switch, and with that circuit open I'm guessing I found the problem with the no fire issue.
And I'm assuming that the way this wire got loose is that when I tried to pull out that starter wire it tangled in the wire to the coil and pulled it loose...and that is why removing the starter wire made the bike not start (with the kick-starter.)
So I'm hoping that this will resolve the starting problem and that the new spark plug caps (which should be here today or tomorrow) will resolve the firing on one cylinder issue, which still leaves the charging problem...