Your plug gap is incorrect; it should be .025.
I assume you have a side distributor, correct?
Cut through the crap. Remove the resistor. Go to NAPA, get a 12v coil. IC14SB.
The coil does not have a "lower" side. The primary wires are marked + or - or BAT or IGN. Just wire the new coil with the negative side to the distributor because you now have a negative ground tractor.
" Question 1: Can the main resistor cause a no start by providing low or intermittent voltage to the coil? I'm not sure how sensitive the ignition + timing system is to voltage drops." Yes it sure can. But as I said, just get rid of the resistor. See tip # 30.
" I'm trying to get it to a known state where it runs consistently before I start adjusting the fuel system. "
I see you've done this stuff before! Some folks would have replaced half the parts on the tractor by now!
" Question 2: The original exhaust was a vertical style with a rather large hole in it. I ordered a replacement that is a horizontal unit. Are they interchangeable? " Yep. They all bolt to the manifold. Best get a new clamp & nuts too.