i've been there and i know what you're going through.
the thing is, it all comes down to a number. a simple number that both sides feel is fair and reasonable. it doesn't matter how you get there, as long as you get there.
however, for you, from a business perspective, you need to have an idea as to what that number represents, especially if it is less than what you should be charging in terms of production + usage. otherwise, you'll end up rationalizing yourself out of business, constantly justifying taking less than sustainable rates. if you are going to cut the number and justify it on the production side, then you know you'll need to sharpen your production skills in order to be much, much more efficient. if you are going to cut the number from the usage side, you need to have a clear understanding as to why and how. otherwise, you'll either be simply giving it away.
i haven't had the need, yet, to buy a photo quoting system, but i imagine the better ones offer a lot more variables, as well as a higher degree of localization (as opposed to "North America"). as such, i use these various calculators to come up with a base number that is probably on the high side. then i tailor it to the situation.
granted, if the photography is really commodity work that won't fetch more than a couple hundred bucks no matter what, even though it should be more like $1500, then you have to decide if that's the type of work you want to do. no different than shooting low-end real estate photos for a cheap agent that only pays $25 for drive-by photos, vs working with a high end agent that will pay $2k+ to produce a portfolio of a high end mansion.
if you use a freelance calculator and determine that your day rate should be $800 and a half-day rate should be $500, and then add a usage of $100/image for 2 years on the web, that should put you around $1100. if they want to use them in print, you can quote them when you have specifics and charge them at the time of use, or you can cut them a deal by paying ahead of time. maybe even offer the images at $75/image and deliver only low-res, web-ready files.
the one thing you have to do is not put your head in the head of the client by "suspecting" what they can afford and thinking that it would be "crazy for a company like this to pay that kind of money". until you ask them, you won't know. they might surprise you. this is what i meant in my original post about "credibility and confidence". if you have credibility and confidence and you tell them that this is a $2k job, they will trust you. if they tell you that you're crazy, then it's up to you to explain to them why it's not. when you show them that it's a lot more involved than just showing up with a camera and taking snapshots, and can show them online examples of the difference between companies that care and companies that don't, you can raise their perception of what you are offering. and, if you can't, then you are probably better off passing on the work.