You have a great idea here. Clustering gives you HA for the instance (memory structure, internal storage engine and background processes) but maintains a single point of data. As far as having many databases, that will pose a management struggle for the DBAs so consider consolidating them based on the various applications and / or app functions (if they are all in use by one app).
That way, you will have fewer but larger databases and you'll have to revisit your storage and maintenance strategy for them.
How many tables exist per database and what are the sizes of these databases? You might be able to consolidate but if not, I'll suggest using multiple instances to manage them (which means changes to the application connection string(s).
Please feel free to reach out for help more via email (firstname.lastname@example.org).