I folded my main wing on my Avistar the other day and have bought a Twist 40 ARF and am in the process of finishing it up. I have dry fitted the aileron control surfaces to the main wing with the CA hinges. The right aileron looks perfect with virtually no gap between the pieces. The other side is a different story. The left aileron surface itself isn't perfectly straight. It touches the wing for about 12 inches and then a gap is created by the crooked portion for about 8" where there's a 1/16" gap, and then it touches again for the last 3-4" towards the fuselage. Is this going to create big problems? Should I try to remove a portion of the covering to sand away the "high" spot on the aileron surface closest to the fuselage?

From what you say it does sound like it will cause problems. Before I would go in to modify and try to fix what you have I would call back to Horizon and let them know about it. Horizon has great customer service and shouldn't have any problems replacing the items.

Hope this helps

Ken