Are we able to upgrade runes from say fine fire rune to an exceptional fire rune and just pay the 5 gold difference?

nope.....

runes don't 'upgrade' they are crafted one way or another

you need to have some one craft a new rune or fine one

That said, bear in mind you can sell runes back for 1/10th their value to at least recoup some of the cost... OR you can sell runes for cheaper to other Heroes. Selling a Tier I Rune for 4Gc and paying the transfer fee of 2Gc to another Hero who wants it costs that Hero 4Gc, and nets you 2Gc. Both Heroes get a better deal than they would have otherwise gotten via NPCs.
Full details on this will be included in the updated Campaign Guide, alongside trading items on CPs (to be worked on after the Errata has been finished up).

Don't sell them..

put them on your back-up weapon...

you should always have one, if you haven't let me stat up some guys with disarm for you

Say that to the guy with a Flamberge. Hauling that thing around limits what you can carry in addition

As told by the Binder who uses one as well.. as well as a dagger (a good place to move the runes) or your armor (remember the same rune can be moved to your armor.. it just changes it's effect)