Hmmm, well, if the crank runout is good and no signs of trouble with the pistons, I'd think about just throwing it back together with new gaskets (I wouldn't reuse anything, especially crank seals, once you've had it apart). I'm no expert on when to replace what, but if you do a leakdown test, that'll give you a good idea of where you're at. If everything looks good but leakdown is marginal, a light hone and new rings would probably bring it back up. As long as it runs ok, I wouldn't worry too much if it's had new pistons. The crank is the one thing I wouldn't chance. If that goes, you'll be looking for a whole new engine. You need a dial gauge, and with the engine apart, you can just set the crank in the bottom half of the crankcase (Polaris has a cradle for that purpose, but I don't see why you'd need that). Spin the crank with the dial gauge set where the taper for the clutch output starts, 1/2" out from where the taper starts on the flywheel side. Polaris spec is up to .004, <.002 is preferred.
Other things that are hard on the crank are a clutch imbalance, if the belt side clearance is too much, misaligned clutch, and bad motor mounts. These motors were pretty hard on motor mounts, they'll definitely need replacement if they haven't been done recently; when they go bad, the engine will pull itself out of alignment under load. Torque arms were a popular add-on too, but I can't say how much good they actually do.
