Well, you could probably do the whole thing yourself. Since the waypoint file is just a database, you could convert this to a simple txt file and then write a LISP routine to read this file, make the conversion from Long/Lat to X,Y and then draw the points in AutoCAD but it seems quite a hassle when this software will do it all for you.
I notice that there is an option to shift all drawn points to a user specified location using the software. I guess you must be using the free trial version. I suggest you have a bit more of a play around with it before looking for alternatives. On the face of it, it looks as though it ought to do just what you want. I don't think $325 is too much to ask for something that could be a great timesaver.