It's a pickle, no doubt. You won't get the SWU back once it's used, so you'll have to call the ball early. The real question is how important is it to you to upgrade the EWR-SFO flight vs. the value of the upgrade instruments. If you do what you suggest -- use a CR-1 for the transcon portion -- and then your SWU clears, you're out a CR-1, but you made sure you got upgraded. You could downgrade EWR-SFO then reapply the SWU to the transpac portion only, which would "save" you the CR-1, but then you're in Y for the transcon. Using 500s is even dicier: At this point, 48 hours out, this will put you at the end of the line for upgrades until it goes to the gate. As a 1K you'd probably be okay at that point, but it's hard to say without knowing date/time/loads. The thing you shouldn't try to do lest you run afoul of the FT morality police is try to swap in 500-mile certs for the EWR portion without having to go to the waitlist.

If I were in your shoes, I'd use a CR-1 on the transcon. If you clear SFO-SYD, you'll be so happy you won't so much mind "losing" the CR-1. If you Don't clear SFO-SYD, at least you got 5+ hours of rest prior to the longhaul, and you'll still have the SWU.