I did this and just grounded the unplugged boot with a alligator clip test lead. (note, I think these new MDI coils have built in protection though. As they have a lead running back from the boot and grounding out under a bolt of your choosing).
Neither side runs great by itself and neither would hold idle. The only noticeable difference between both sides is that when #1 was running, I was getting black sooty exhaust (noticeable). Whereas the #2 did not. I suppose this is to be expected. Edit: I realize though, that with black soot coming out of #1 under a no-load situation, it confirms that this is indeed a motor problem and not a loaded hydro (or other external) issue.