These are the things that should be optimized (but i guess Krun!x already optimized them)
optional: acp,memcache
configs: myslq (my.cnf - query cache size, key buffer, etc), php (php.ini), change apache to nginx or lighttpd
wordpress: hypercache,super-cache,w3 total cache (choose one)

Also: are there any new plugin installed? I remember that when my wp-admin loaded really slowly, it was because of a plugin/cache error. Create a subdomain on your server, replicate your site and start to experiment with enabling/disabling plugins. If - as Krun!x said - your load is normal then you can experiment on a subdomain (as the server is not overloaded).
Try site load !without! caching engines... i think there is some collision between caching engines.