Pricing is a complicated topic (or can be), and I don't claim to have mastered it myself. In fact, I'll freely admit that I'm still struggling to figure out all of the details of our pricing model for Fogbeam. There are literally dozens (or more) books written specifically on pricing, so don't feel bad if it all seems challenging.
That said, here are some thoughts based on my own experience and research.
Keep the model as simple as possible (but no simpler?). Nobody wants a complicated pricing model with per-core charges mixed with CAL (client access license) charges, mixed with varying discounts and floating license servers and blah, blah, blah.
The challenge, of course, is how to balance having a simple pricing model, with your desire to charge companies based on the value you provide them. That is, a larger company with more users is (presumably) getting more value from your software and should pay more. So charging per user is a valid option, but it's not the only one. You could charge based on the customer's revenue, or scale the pricing based on the hardware (physical or virtual) required to run the software for their needs.
There's some really interesting stuff in Douglas Hubbard's work on "Applied Information Economics", although I don't really have time to try and explain it all here. But the key of his approach is to try and actually quantify the value of an information system by figuring out a way to measure the factors the system will impact, and then figure out the economic value of improving those factors. That's a little bit of an over simplification, but it's an interesting approach built on calibrated estimation, monte carlo simulations, and elements of modern portfolio theory.
I'd recommend reading the book How to Measure Anything by Hubbard, and/or read the Wikipedia article on AIE[1] and see if you can think of a way to apply this with your customer(s). Ideally, if you get them to buy into the model you create, you have very solid footing for establishing the price of your software, since you can actually put a number to the value it adds.
There's probably a heck of a lot more to be said about all this, but it's bedtime here. :-)
[1]: https://en.wikipedia.org/wiki/Applied_information_economics