Did the Six Days originally come as a homolgated unit? I've seen the restrictor plates in the intakes and exhaust and those would be enough to choke anything off.
I'd also want to check the integrity of every wire in the harness, including the grounds. The previous notes regarding the connectors were good advice as well. The uneven idle sounds like it may be related to air leakage, but ... the best post was the one that said it's impossible to diagnose a problem over the chat room.
Your problem is likely going to be resolved, and when it is it will be a small consolation to the headaches you've experienced. For perspective though you could have bought a Husky 125 instead and been chasing jetting and bog troubles, or a Kawasaki 250F and been wondering why you've got 9 gears in the tranny, or had a piston crown snap off in a KTM ... Check out KTM Talk or CafeHusky or ThumperTalk to see what other bikes and brands have issues.
These forums are great because they allow the free exchange of ideas and information, but they tend to magnify problems too. Hopefully we'll all be reading about how satisfied you are with your bike and the people that helped make it right in a very short while.
If you're convinced your bike is not going to work, maybe I can work out a deal with you on a new XC300 ... something to think about.