Information on setting up a server can be found in
this sticky.
Cost-wise, if you're seriously contemplating an IRC network made up of 40,000+ users regularly, you're looking at a largeish amount and you'll need more than one server. That said, many ISPs/Universities are willing to host IRC servers.
The bots issue is more complex. Botnets are not something we'd help with, and it would be much more efficient of you to run a Services (Nickserv/Chanserv/Memoserv) package on the network anyway. Such packages are usually free, popular ones include
Anope and
Epona. Customising them would require help from their relevant development teams and most likely advanced knowledge.
Halting private messages is breaking protocol, you'd need to edit the IRCd (or create your own). I think some existent IRCds would allow blocking of the DCC protocol already to prevent file sharing, again, you'd find it more enlightening to ask the IRCd developers.
My question is, can all of this be developed easily, and also how many irc ops would it take to control the entire server, responding only when needed to handle issues?
Possible? With enough effort, I would guess so. Easily? I'd guess not.
Large networks tend not to have a set amount of IRCops - they let individual server administrators choose which IRCops they want, though I find most servers don't have more than 5 IRCops (and a lot of the time less than that). As long as you have enough IRCops to cover the different timezones, and there must be 2 or so IRCops at all hours, you should be okay. If you're looking for user support and IRCop interference in "alliance"/channel issues, you may need more.
Regards,