I'm not going to pretend I understand the database structure and optimizations there, but on a basic administrative level - is your hosting optimized for the kind of traffic you get? Msql and Apache (if Apache) are rarely ever set up on VPS for 'real' traffic. Also VPS vary tremendously in quality and configuration etc. What is causing the issue? The database size? Parsing tables? Memory usage? CPU? Honestly, compared to most standard php/mysql forum applications MLF is pretty low fi and very tweakable.

Mlf uses barebone PHP (no framework) and is performant. What kills mlf in the end are the DB queries. From what I've seen an average shared hoster installation get's into trouble around 1500+ users and 300.000+ entries, which is admittedly not so "little" anymore.

Mlf also caches rendered HTML in separate tables, which is O.K. if your DB is small, but contributes to the DB bottleneck in the long run.