it doesn't matter... you'll probably get less bids if you start the item at the minimum you want to sell it for... i always start my auctions at $1.00 and they'll still sell for what they're worth on ebay.
The fee was deducted when you accepted the payment, since you have a premier account. There is no fee for withdrawing to a bank in USD, as far as I know. The payment fee is 2.9% and $0.30 per payment, as far as I recall. As far as the only way to avoid it...downgrade your account or don't use PayPal.
Not really. The insertion fees only vary at most by a few bucks. The end-price fees are where they gouge you, not on the $.35 or $1.00 insertion fee.
Generally people start auctions at $.01 or $.99 because it creates a base of bidders at the very beginning who will check back on your auction all the time, and some of those people will be the type who'll end up paying more just to "win" the auction.
So if you start @ $.01 you'll have 10 or 15 people bidding when it gets to the REAL selling price, whereas if you start it right below the REAL price you may only have 5 bidders. Odds of one of those 10 or 15 being that guy who's going to pay more to "win" are higher than one guy in 5.