* 1) If live, would Aido buy/sell RUR first and fix the above? (it's running in simulation so I understand if it can't change the wallet data)

No. If I understand the question correctly, it would be buying RUR only to sell them again?

* 2) With my home currency set at USD, and BTC-e not offering direct RUR/EUR trades, would the system do point 1 if it weren't simulation?

No.

* 3) Do I need to hold multiple currencies (including BTC) in order for arbitrage to work?

Yes. You need to have a balance in the selling currency wallet.

Also, as an aside, can Aido work with LTC instead of BTC?

Not currently.