Having aftermarket wheels and having lowered the car gives an alignment shop an out if they don't want to be bothered with you and/or your car. They can just claim that the modifications are preventing them from being able to align the car properly, and if they do, there's not much you can do about it. Be ready for this if it happens; Don't let it catch you off guard or upset you. Assume that they are interested in helping you out with your car and keeping you as a customer, and go in expecting the best. Just be ready for the worst, just in case.

Are you allowed to go into the work area and talk to the alignment tech directly? If so, I'd go in and discuss the alignment with him. I'd wear my humble suit, and explain that the people in the S2000 owner community all seemed to think that, based on their experience, that WE might be able to get the alignment sorted out a little better, and I'd ASK him if that might be the case. No telling how he might respond. He could just ask you, "How does the car drive? Any problems?" or he might just say that this was the best he could do, given your mods. If you are lucky, and he is good at what he does, he'll likely be receptive to the idea of trying to get the car aligned better, but if he's already worked his tail off trying to get it right, and failed, he's not apt to want to try to make it any better. I'd talk to the guy and feel him out, and if, after doing so, I felt that he might actually be able to get the car aligned properly, I'd let him try again.

LOL, either that, or I'd take one look at the specs after his first attempt, get pissed, and just take the car somewhere else. Sloppy work can sometimes get me pretty upset, and this has the look of sloppy work.

What you really NEED to do is find an alignment shop that is willing to work with you, and deal with your modifications; The guy CCR uses does lots of work on race cars, including open wheel cars, and he both understands the importance of accurate alignment, and is willing to put in as much time as it takes to do a proper alignment. You really need someone just like that doing the alignment on your car, but there is no way I can help you find the right shop. Maybe you could check with other S2000 owners in your area and see who they use.