Are you insane? The guy has had a PC for 2 years - it's worked most of that time, and now it doesn't. But he won't send it in like they ask, just stomp his foot when...big surprise...the onsite doesn't work. They could have done better with the IO shields, but this does seem like ASUS had some blame too. You seem to be making this hard on yourself, too, OP.
Uhm, no. The OP clearly stated that it has never functioned properly with regards to playing games. Which presumably is the point of purchasing it.
Secondly, Velocity Micro is very squarely at fault. Sorry, but I did OEMing. If you extend a promise of warranty, you assume liability for replacement of identical or equivalent parts under the terms of the warranty. That's not my take on it, that's the legal take on it. If VM wants to swap the Asus for an equivalent Abit, they're within their rights. But they can not refuse to replace a part because they can't get it.
Which brings me to my other point; what makes VM any better than the guy down the street, if their warranty is no more than the manufacturer's warranty? In fact, the OP could have RMA'd the board himself faster than VM. It is VM's responsibility to ensure availability of replacement parts, independent of the manufacturer, as part of warranty obligations. Period. Not having a replacement or equivalent part is not an acceptable excuse. And forcing the customer to wait for an RMA through the original manufacturer is just bad business and bad planning.
And yes, I am well aware of availability guarantees - or rather, the lack thereof - from nVidia, Asus, AMD, etcetera. It is the builder's responsibility, as part of extending warranty, to ensure availability of parts. If a customer has an AMD Athlon64 3000, and it fails within the warranty period, the law does not care whether or not AMD makes it or the builder can purchase it - the builder's warranty specifically grants them the option of making equivalent replacements at their discretion and based on availability.
Frankly, it sounds like the OP has been given a lot of runaround because of VM's exceptionally poor planning. By repair two, VM should have given the OP an equivalent working part. Key word here, working. If Asus does not include I/O panels, it is a builder's responsibility to either A) have the customer retain theirs, or B) provide a replacement from stock or purchase. If Asus can not provide a working motherboard, then the builder should provide an equivalent replacement. It is not necessarily the builder's responsibility to replace the entire system, only to provide a working system of same or equivalent parts, as within the warranty terms they billed the customer for.
Bluntly, my opinion on the matter is this; VM has given the customer a lot of headache, runaround, and excuses - including here. The customer has made reasonable effort to be accommodating, and VM has failed to take advantage of the opportunity to resolve the matter. At this point, VM needs to just bite the bullet, and send someone out to replace whatever parts are necessary with equivalent or better to provide a working system - that means motherboard, and CPU and memory if necessary - for the OP.
But hey, just my $0.02 from my years of building.