I guess I wasn't trying to throw you under the bus...but if you've sold them before, I'm not sure why this is a "hard time". You would just price them the same as you always have...and if you feel like they deserve a better price because they ordered several (even though it's a rush) knock a little off.
It also sounds like you've already started on the job, so the quoting process was either a moot point, or you used your formula and it wasn't as much as you thought it should be once you got into the job.
I base my sqft price on the the customer. If the person is nice, has the ability to check email for proofs, and doesn't have to stop by or call every time I have a question or they have a question, they get a better price...if the person doesn't carry a cell phone, can't check email, and isn't able to work with me easy...the price goes up...but I'm still basing it close to my original dollar amt that I charge for "standard customers".
I guess I just assumed that a sq. ft. price was the easiest thing to price even if you'd never done it before because there really aren't too many variables in a banner quote. Get as much as you can w/o losing the job. You never leave money on the table...even for a banner. If you don't know yet what the market can bare, then do what the others suggested and call around I guess.
