1) I am assuming you want to go for tourism
2) Check everything I say yourself
3) Yes, one visa for whole country. If they still ask for destinations/towns to be visited, then include anywhere you might go. But IME you don’t get problems being in Perm if your visa app only said Moscow.
4) 3) doesn’t apply to freaky/remote regions like Chechnya, Yakutia, oil/gold towns, but if you’re going there, you’ll have a local advisor anyway.
5) you need two payments for a Russian visa: someone to invite you (which you will pay for if you’re not their guest) and a processing fee to the Russian government. This probably explains why you’re seeing two different fees.
6) Cheapest/quickest reliable place for invitations is http://www.visahouse.ru – all done online iirc
7) There are different fees for processing: multientry v single entry, 24 hour/instant processing v 3 week processing etc.
8) When you get to Russia, you are supposed to register your visa with the local cops. In practice, your hotel will take care of this for you.
Good luck…