The way I read the rules, drip rail removal puts you in /Alt and mounting windows flush with outside, if they were not there in the stock configuration, puts you in /CC. You would normally run Classic if you want (don't have to). At the outset if this is a new car/proposition for you and considering your concern that the modification may not give you much, I'd suggest not going to the trouble, build your car to whatever class you want otherwise, run it and see what you get. If you then want to step up the program to the normally faster classes, go for it. Some of what you want to do can be simulated in a wind tunnel (tape, cardboard etc). (where do you live? The A2 in North Carolina can answer these questions within an hour or two. )In addition to someone here having first hand knowledge, some searching around you might find some information that answers your questions directly.
Oops, see you are in York, Pa. The trip to NC is not too bad if you really are serious about this. I have done it from here (Annapolis, MD)
Additionally if you are thinking ECTA and running /RS or /SS, no body cares what you do to the body, in essence.