What happens if you expel the Jews

You cannot split an individual unit (i.e. a levy from a single source). The manual doesn't come out and say it, but this dev diary talks about it.

One way to get a smaller individual unit would be to send the troops to non-friendly lands (i.e. not yours or a vassel's) and then dismiss them. But that might not be possible since you probably don't have any non-friendly territory to which you can march the troops.

@Paul Marshall's idea of getting more ships is also good one. Maybe there are mercenaries navies you can hire to transport your large levy?

As far as I'm aware, the tax income and levy size you get from any vassal are based on their holdings, and modified by your realm's taxation/levy laws and the vassal's opinion of you (for taxes at least - I'm unsure whether opinion influences levy size). Catholic Bishops have the added complication of paying their tax to either you or the Pope, depending on who they have the higher opinion of. I don't think a vassal's statistics influence any of these things.

Pretty sure any male of your court can be appointed to the role of Court Chaplain - on appointment the character's portrait will change to show them wearing religious garb.

You're right that making unlanded son's Bishops counts as giving them land. Be careful with this though, as once made a Bishop your son is not eligible to inherit other titles from you in the usual way. If your main heir has an "unfortunate accident" you may find yourself suddenly lacking an eligible a successor!

For realms smaller than Kingdom, any lord can appoint a successor for any Bishop that is his direct vassal. If no appointment is made, the new Bishop is appointed internally by the Church (or Pope). Larger Catholic realms must opt for one of either Free or Papal Investiture - Free operates as before but angers the Pope, while Papal gives the Pope sole control of Bishop appointments in your Kingdom and grants you the Pope's favour (useful when seeking to excommunicate rivals, divorce wives and so on).