I always line up my degree wheels with the stock TDC/F mark on the flywheel, which on the RC aligns with the parting line of the cases when the piston is @ TDC.
But that's not it, so no cookie for you.
Sorry, forgot to answer the breather Q. Short answer, I don't drill the cases for an additional breather. I do sometimes drill out the breather nipple on the valve cover and use a Ducati corsa reed valve in the (big) airboxes. That seems to work pretty well.