Does anyone know what the process is for getting upgraded at check-in/gate with a coupon? Will I get upgraded if there is availability at check-in, and who do I ask? Have been waitlisted since September for a flight this Friday.

It will be automatic (normally): if there is space available, the coupon will clear 2-3 days before the flight (normally). if you try a dummy booking for your flight and there is still business available, you should have good chances for an upgrade (unless bidding or an earlier coupon beats you).
But most probably, if your coupon doesn't clear, there will be no space anymore in business at check-in. However, in rare cases (e.g. no show) this could be possible - but I assume it would be the gate agent who handles it then.
I only had one instance where there was a free business class seat during the flight despite at least 2 coupon upgrade requests (my wife, plus another passenger who complained to the cabin crew about it).

One time I tried to use a coupon, it waitlisted then two months later my girlfriend joined me on the trip, I tried a coupon on hers and hers cleared after 48 hours. My request remained waitlisted though, and finally, I didn't get an upgrade.

There was plenty of J availability and the crew invited me up to sit with her, which was nice of them.

It does make me wonder whether leaving it waitlisted for months reduces your chances of it clearing though.

Well - I had quite some requests that were in for several months and in the end cleared 2-3 days before the flight...

Seems I am unable to check in. On checkmytrip status of upgrade has moved from "waitlisted" to "unknown", original ticket still showing confirmed though. I guess the upgrade should process.

Not knowing your itinerary one explanation could be married segments. If your flight was XXX-ATH whereas your girlfriends's was XXX-ATH-YYY then availability could be different, which could also impact waitlisted upgrades.

when an upgrade is cleared you will get an email with updated etix, did you get that email? :)

You do not get an email sometimes. Actually most of the times i did not take one.

Is the rule still that the cheapest P fares U and T, with no cases, cannot be upgraded with the vouchers?

Yes...

It depends on the fare type. When you book GoLight then PUT fares cannot be upgraded. But when you book Saver or Flex they can.

I am 72-48 before flight, business seems wide open on both flights.
Anywhere I can call or something else I can do to het wait list cleared?

Unfortunately, only praying... :)

Thanks

Will checking in online have any effect (positive or negative) on the upgrade chance?

One possible advantage of OLCI (in addition to the standard ones) is that if they decide to upgrade you after you've done it, they do a "regular", non-coupon one, which not only leaves the coupon untouched but also yields tons of miles. It has happened to me 3 or 4 times, but I'm not sure that your chances for an upgrade are increased in any way. But do it, certainly no harm (I guess!).