Ah then judging from everyone's replies it does seem to be a matter of speed.
@jact Sounds like it is on the DB side then. I would love for someone that's having speed issues to contact me and let me take a look. I would, of course, sign an NDA and I can supply a whole list of references if you'd like as I know the data is sensitive.
I also invite TMM to contact me if they have a system already setup with a large amount of data and can simulate high usage. I'd love to help out. Are you guys looking to hire a CTO or Senior PHP developer?
@robwod It sounds like v4 could use a bit of display:none/block action to hide/unhide content areas rather than refreshing the entire page. Perhaps some repopulating of select boxes and things based on other selections to avoid page refreshes as well. I'm sure some AJAX would also go a long way to minimizing requests rather than running a whole page worth of queries over again... and like you said. Remembering previous preferences would also be nice for that area.