Everyone is going to have a different opinion. Here is mine.
I believe the problem is in your attitude.
For most of us on this forum, putting together a computer is not difficult. For some people, maybe it can be or they do not have the time or will to learn how to do it. It isn't that different from you going to a mechanic or hiring a plumber or any other specialist. You make a deal with them and are OK with them making a profit as long as you get the work done you were expecting and hopefully get some good insight on how to prevent it or how to better your situation. They are hoping to benefit from some of your expertise apart from just getting the service.
There is nothing wrong with you making a profit. The problem is in the way you are trying to do it. Your first set of numbers was about $435 in parts with the intent of charging $500~$600. What would be nice is to think of a decent setup of good current parts instead of the mish-mash (really, that is what it is) of crap parts.
Something along the lines of a Regor or E5200 paired with a SB710 based board or G31 and 2x1GB (or really just 2x2GB and raise the price $30). Not only are you getting a lot better performance, you also get an upgrade path to quad cores, a warranty and probably lower power consumption (definitely, when you compare it based on work output). A decent entry level gaming card (at a reasonable price). Those change but currently it seems like it would most likely be a 4670. You could build a computer around those parts for about the same price.