Another thing to check is the battery and cables.
You said you checked the battery, at the terminals?
Check it again using any ground, a bolt on the engine and also anywhere on the frame.  If you got a flaky ground, the reading will vary.
You can also check the positive lead, but it's a little tricky.
With the seat off, pull the rubber cap off the relay, one of the big wires goes to the battery.  And with the key on, you can check the headlight leads.

springman wrote on 09/12/21 at 20:15:28:

penetrating oil, to make it easier to get out.  might need to soak it to loosen corrosion.

I finally had a chance to work on the S40 this weekend. It is embarrassing but I will man up. After taking the tank off the bike and looking at all the wiring with nothing looking bad I finally decided to take the battery out and put it on my digital charger even though the load tester indicated 12.81 volts. The load tester sucks. The battery was discharged so I charged it and after I finished I put the load tester on it and it read 12.95 volts.   So I installed the battery, hit the start button and it cranked just fine. I put it all back together and took a ride and it worked just fine.

Moral of the story is. If it doesn't feel or look right. Trust your instinct. I knew I should have taken that battery out from the beginning.

Well, the bike now has a pigtail on it to connect to the trickle charger.

The headless bolt I removed by spraying liquid wrench on it each day for 3 or 4 days prior to working on it. I then drilled a hole into the headless bolt and tapped a hex wrench into the bolt . It came out fairly easily. Thanks all for the help.