There's no reason to think the alternator is bad, since it's not part of the starting circuit. But you'll find out for sure once you fix the starting issue.
My guess is there's a fusible link or fuse blown somewhere. Or it might be a ground strap between the chassis and engine. But you could have damaged something else. I know nothing about Hondas and their starter circuits, but my guess is there's a relay somewhere on or near the starter that gets power from the battery and the starter switch. So that's the first place to look: Probe the terminals on the starter relay with your multimeter (on volts) while a helper turns the key. Use the starter or engine as your ground. If you don't get any voltage there, retry using the negative battery terminal as ground. What you find at the starter relay terminals should give you an idea where to look.
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Today's Featured Article - Third Brush Generators - by Chris Pratt. While I love straightening sheet metal, cleaning, and painting old tractors, I use every excuse to avoid working on the on the electrics. I find the whole process sheer mystery. I have picked up and attempted to read every auto and farm electrics book with no improvement in the situation. They all seem to start with a chapter entitled "Theory of Electricity". After a few paragraphs I usually close the book and go back to banging out dents. A good friend and I were recently discussing our tractor electrical systems when he stated "I figure it all comes back to applying Ohms Law". At this point
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