PNRs can not be linked at all...doesn't matter if its award, revenue or any combination. Furthermore, these are two separate airlines.

As to your bag question, I would think that with an overnight layover, they won't tag them through. I could be wrong, though. Either way, you are going to have to pick them up in SFO, as already posted, to clear customs. I would say you are better off with the overnight layover if on separate tickets - as any delays causing you to miss flights on the second PNR and neither UA or AC is required to protect you. So giving yourself the extra time is probably the smart thing to do.