SaaS platform with 10k niche users and a large company wants to buy a custom version. How do you model a cost structure beyond hourly?

I've run in to this over the years which is why I run a custom development company but we make products for other companies and one has run in to this problem. They are a SaaS company and target individuals as well as small groups. A large group that represents a lot of individuals has reached out and asked for a version of the platform that has some unique logic and workflows specific to how they manage their constituents. Conceptually these modifications can not be made to the core platform so we need to come up with a way to effectively price this arrangement. We would host and own code basically as a SaaS platform unwise to them. Primary concerns How to charge for more than just modification hours. Impact of branching the platform long term with upgrades etc. What have other smart people done in similar situations. We are reluctant to pass on the deal because of its head count and symbolic "lighthouse" name power in the industry.