Perhaps you should consider going to the store. I used to work in one of their stores (5+ years ago), and in my experience, they assemble these "prefab" computers themselves. If you need another motherboard, they can simply change it.
If these systems are indeed prefabricated (assembled in a Mycom store elsewhere), you could order a custom PC.
If you go for a custom PC, you could pay a bit more or a lot more. It all depends on what you want.
I suggest you make a list of the things you want from your system (including the price) and take it to the store.
As for your last questions:
- Why do you need a parallel port? Is that for an external sound/music box? Or is that just for the printer? The 720C probably won't work with Windows 7.
- What do you mean by "Ata" port? Do you mean an IDE port (PATA) for your older harddisk or something?
- DDR3 should be faster than DDR2, but it's difficult to say exactly how much faster. It depends on the software: where's the bottleneck. If you need to read and write large chunks of data to a relatively slow harddisk, your really fast DDR3 memory won't help much.