So I have 2 sites running on one dedicated server, one site has over 40k users the other just over 12k. The site with 12k users runs ALOT faster than the site with 40k users. The server has 8cpu's and something like 8gb ram. Both sites run well within the server resources i.e never maxes out and is far from doing so.

Is there a way I can speed up our main site? What about database pruning?

Any suggestions on what I could do is greatly appreciated.