So I'm trying to build some decks from a collection I bought. I have exactly 3 of everything except for Contested Village, Warpstone Excavation, and Innovation of which I have 9. My question is, other than moving those staples from deck to deck, are there other options to replace them? Maybe a decklist without using them at all?

Well, for tournament decks, Warpstone Excavation and Innovation are on the restricted list, meaning you can have one or the other, but not both. Every deck still runs Contested Village, so you just have to proxy them if you want to have more than three decks constructed at once.

I run into this problem too. When I get a deck the way I like it, the deck will stay sleeved in a box unchanged for long periods of time.

Depending on the deck, I find Bottomless Mine to be pretty good. I works well with if you have lots of low cost units.