Claire
Your health and your personal comfort are both matters for you. As you say in your post the ground staff and cabin crew seem to have gone out of their way to help you and make you as comfortable as possible.
I can't think of a single reason why the airline would want to upgrade you in the circumstances you mention in your post.
In fact I can think of three reasons why they might not want to upgrade you, viz:
I tried for an upgrade at check-in,
...at the gate
... and on the plane.
You say "I don't expect an upgrade as a 'right'," but unfortunately that seems to me exactly what you seem to expect.
Sadly I think your expectations were and still are wholly unrealistic. Expect to get what you pay for and be happy with that; should an airline give you something more then that is a huge bonus and be thankful for it.
So for the return journey you will know what the likely pain level will be in economy and you will know how much money you will have to pay to buy the upgrade to get the more comfortable seat you want for a relatively pain free return journey.
The choice is yours.
Finally, as a previous poster mentioned, upgrades are for operational reasons only and are commercial decisions taken by the carrier.
Even if the airline was offering upgrades on your particular flight, just because you are in pain is not a reason for an automatic upgrade and they could just as easily upgrade someone else ahead of you.