Yea, if it's a stock stroke '86 crank (short rod) the cylinder should bolt on without a spacer plate. Have you tried any of the spacers to see if they'd work? Perhaps the person you bought the bottom end off from told you the wrong crank.
As far as those front base nuts, I think you've figured out about the only way to get to them. That's how I ended up tightening mine, grinding down a wrench. It sucks because you can't accurately torque them. Just make sure and get them tight
