Well, as I just got done saying in a different thread here, I'd bet money that the problem isn't so much Vista as it is you bought an HP system. All versions of Windows have been in need of seriously revamped fault tolerance. For every improvement Microsoft has made on that front over the years, Windows still trips and falls entirely too easily when it encounters poor quality hardware. If you had Linux running on that system, it might not be as stable as it would be on a system with better quality hardware, but Linux would likely just stumble where Windows would trip and fall.
So in the future, don't touch HP/Compaq systems even with a stolen 10 foot pole. There is a reason they are consistently some of the cheapest systems out there, and that's because the hardware is crap. In general with computers, lower prices means lower profit margins. Lower profit margins means more corners cut in the production to try and save a few pennies on every system. Ultimately that results in shoddy hardware, which has been a staple of HP/Compaq systems for over a decade... Dating back well past the time when HP and Compaq were separate companies. This really shouldn't be news to anyone. HP and Compaq systems have always been infamous for being steaming POS. If you buy one, you are almost guaranteed to be sorry.
So, I'm not saying that Vista isn't without any blame here, just that I suspect you're blaming Vista when you should be blaming HP. Especially when you're comparing it to a Shuttle system. Shuttle is a very low volume, specialty system maker, sort of like Apple. Like Apple, they charge a premium for their systems, and some of that goes to increased quality control compared to the bigger volume vendors like HP/Compaq, Dell, Gateway, etc.
Lecture aside... What is "everything" that you want to transfer back to the other system? Things like video files and photos are no problem. Programs you probably want to just forget about.
Also, if things didn't work right after paying close to $400, why did you not demand either a refund, to have someone come out again and again until it does work right, or both? You paid for a service, and from the sound of it, did not receive the service you paid for. So you should either demand the service you paid for or your money back.