These days it seems you'll need to be a bit more exacting with your pricing to reflect comparable sales, or whether you would do another one for the same price.
It helps to keep track of your materials expenses, of course, but also your time spent exclusively on the model, the costs of running your shop while making the model and any additional costs that may apply. You'll probably be asked to justify your hourly rate. Don't forget to add transportation or shipping costs.
I guess the bottom line would be what a model of similar quality would normally sell for, as well as what the museum will agree to.
Like with auction shows like "Antiques Roadshow," their bottom line is with replacement cost. If you can figure out what it would cost to make another one, including allowances for inflation or rarity, then you'd have a ballpark figure on value.
I'm not a lawyer and it has been a few years since I did commission work, but these are things to consider.