I bought a K fare SFO-EWR-GLA for travel 12/30. (return date is V fare). There are upgrades available to BF on the EWR-GLA portion but of of course the SFO-EWR is waitlisted. Is the SFO-EWR likely to clear before travel. I am silver so I'm unlikely to get EAU in the alternative.
Would you upgrade the international section and wait for the domestic portion?

You don't upgrade each segment - If do a international upgrade, your US segment will be upgraded also.... If I understand the question.... At least that is how it has always worked for me...

I usually fly with NW so this would be my first time upgrading with CO. But from what I understand the agent told me today, I can go ahead and upgrade but the domestic portion isn't available. I will definitely get upgraded on the international section but I may never clear the current waitlis on the transcon but I will be debited 20 thousand miles regardless. The international flight is about 7 hours so it's probably worth it.

Hmmm. I'd say the 20K miles is definitely worth it just for EWR-GLA, especially if it's on a 757, you don't want to be in coach.
You'll have to chance it on the SFO-EWR leg, but usually mileage upgrades are at the top of the waitlist. This is a tough route, though, lots of paid F, though I doubt anybody pays full Y and gets free elite upgrade since they have non-Y fully refundable tickets for much cheaper.

I would check the availability periodically (you can use http://flyaow.com/classamex.htm) and keep an eye out for inventory in "F" class. As soon as you see the number next to "F" >0, call up CO and make sure they clear you into First. Their computers aren't always so swift.

Good luck.

Good news for you. I believe that mileage upgrades have TOP priority for standby upgrades. CO will hold from EUA a few seats for revenue on the SFO-EWR portion, so no matter who is flying, you should be able to snag one of those if you check in super-early. Just make sure that when you get the upgrade issued, they acknowledge that you are entitled to an upgrade on the domestic portion, too, when it becomes available. And when you check in, make sure you're on the standby list for the upgrade.

My brother flew ZRH-EWR-SFO last July and we did this exact same thing. In the end, he got the EWR-SFO upgrade.

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NW Gold, finally!
Elite since the year I started making my own travel plans.
NYC since 2000

EWR to GLA is a 762 (at least for this winter) but, from experience, worth the upgrade