Ya, custom built applications would cost a lot more than something off the shelf because you're making it specifically for them and you would have to fund the whole development from what you can charge them rather than funding development yourself, and then selling it for much less, but to many more customers.
The only real way to put a price on it would be to work out a realistic estimate for how long each phase of development (specification, design, development, testing, implementation, changes and stabilisation, etc) will take, and put an hourly rate on that, and then work out a service level agreement for support, and put a price on that, maybe get them to pay a retainer for a certain number of hours per month at a discounted rate, and then have a higher rate for overflow.
