What is the optimal approach for configuring an application to support 1000+ domains/websites?

We have developed a website platform consisting of approximately 1000 websites across 1000+ domains. These websites are tailored to small business owners and are relatively straightforward, typically consisting of only a few pages.

The websites make use of one application, set up with Elastic Beanstalk. Every website has one or more domains.

CloudFront has a limit of 250 instances per AWS account.

What is the best way to configure: CloudFront (incl WAF) and Certificates?