Honestly, I'm not exactly sure how you could have prepped the stove so it would have passed muster. Any solvent used to clean it will likely be flammable, and soap and water doesn't solve much of anything. All you can do is wipe it down so it "looks" as clean as possible.
So what now? I agree the Apex II is a reliable but porky stove. You could always just get another one ($65; www.coleman.com). Or, go with a new, light MSR SimmerLite ($90; www.msrcorp.com). This is a very nice stove, and MSR stoves are generally very reliable, although not as heavily made as some other stoves. (I've enjoyed 20, problem-free years using MSR stoves.) For a really nice stove, try the Optimus Nova ($130; www.rei.com), which may be the best liquid-fuel stove on the planet right now. But then, at that price, what do you do when some other airline security guy confiscates it?