Hmmm a tough situation.
Well as has already been said - you can't ask for an exit row because of safety - so my idea would be to ask for a bulkhead seat that might have more leg room (depends where this is depending on what A/C your travelling on) calling the airline and explaining your situation before hand is a very good idea though, it worked for my mum who is also disabled.
Is it just the legroom that bothers you? A lot of passengers bring on special cushions etc that help their journey to be more comfortable.
As for the upgrade....well....my advice is if you haven't been given an upgrade at check in (no harm asking there - maybe keep an eye out for a floor supervisor before you even get to the desk) then take your allocated seat and try to catch the attention of a kind looking crew member and ask if there is an available seat that would be more comfortable (but don't ask for an upgrade), expalin your situation to him or her and see what they come up with. Hopefully they will take pity on you and upgrade you to a more comfy seat.
What I would say is not a good idea is asking as you come on board. This is a busy time for your in-charge crew member and they could dismiss your request along with all the others they get for an upgrade every day.
I'm not saying that your crew are not sypathetic to your situation then or at any other point if you don't get an upgrade. However problems arise when one of your fellow passengers who is a Gold card holder (or whatever frequent flyer scheme your airline has) spies your movement up the classes; they will also expect the same treatment - and if they don't recieve it will want to know why when they are spending so much money on their ticket (which are normally full fare flexible etc etc etc).
Good luck anyway and I hope this helps.
