There is a Polaris dealer right by where I live so I stopped to talk to them about jetting. They told me they can't remember ever messing with the jets on one of the 90's. They were really concerned that maybe the crank seals were letting in additional air. Do you think I could check this by spraying carb cleaner around the seals?

 

Best way is to do a leak down as it can tell if the crank seals,head gasket, base gasket,intake manifold or even the engine case itself is leaking. As far as checking the seals you basically have to pull the stator, along with the clutch on the other side. You're already there,might as well replace them.. Soapy water can help,possibly you can spray a little around the right hand seal,gaskets and engine case while under pressure and see if you see any air bubbles. Under a leak down test it must hold around 7 psi with no drop in pressure. Here's an example.