If you decide to fly from Chicago, I find that Aer Lingus usually has the best rates. Not always, but more often than not. And for international flights, iirc, I was allowed two checked bags.
As far as getting to Stornoway, again, I think you might be farthest ahead to buy (or at least get a long-term rental) on a car, then take the ferry. If you get to Lewis without a car, you'll find it a bit difficult. However, if you do decide to fly to the islands (now or in the future), just book a separate ticket, rather than trying to get one straight through. Flybe have flights from GLA to Stornoway for as little as 25 pound, one-way (depending on the day/time). Much cheaper. (Though you can sometimes run into issues with baggage allowance, because they're such small planes. If they can't fit all your stuff, they send it along on the next flight.)