I do not know about the issues you have heard about the Julie, but they are definetly supriour to the Kona's V-brakes in terms of performance. Avid's as such however are pretty much the best you can get out of V's, I had them on my last three bikes.
Now, technically speaking there have definetly been issues with the Julie. They are supposed to be self-adjusting, which for a while has not been the case. A friend of mine has this problem on his 2001 Canyon (German brand, if i remember right), but Magura should have figured this out by now. The workaround is pretty straightforward easy, too.
I have the CAAD4 frame on my '99 team, when it was the last cry. I don't know if they are still handmade as they are not top of the line any more.
I can't tell you if the Coda parts suck as everybody says, i custom built my CAAD4 with the mentioned Avid breaks, all XTR, Synchros and Race Face, but C'dale appearently phases Coda out anyway. There's not much i can tell you about the Kona, it should be pretty rugged, as it's been designed for the British-Columbia crowd, and sure has a hight cult factor. As far as the forks go, the Bomber is a solid and proven choice, the Headshok's unmatched lateral stiffness will win anyday, even though hardly maintainable do-it-youself, and aftermarket upgrades are virtually not available.
For both C'dale and Kona there's one issue to bear in mind: You pay a penalty for oversea's productions. So why go far? Principia for many years has made exceptionally light HT frames out of Denmark. I always wanted to try one, but never had a chance. www.principia.dk
The MSL Pro for sure is a great basis to build up a bike from scratch (or have the dealer build it for you). You can start off with solid parts, and upgrade later. Top of the line and matching the light frame would be the following setup, propably going over EUR2500 however, but except Shimano all parts from Europe:
Wheels: Tune Sonderlaufräder superleicht
Tires: Michelin Wildgripper
Crankset: Shimano XTR (note: one piece, expensive to replace)
Cassette: Shimano XTR
Seatpost: Tune Starkes Stueck
Shifters, Derailleurs: All XTR (I prefer XTR Rapid Rise over Rapid Fire)
Breaks: Undecided, why not Julie?
Fork: Undecided, sorry, Headshok's don't fit inside the Principia's front tube
Saddle, handle bar grips: matter of taste
Pedals: Time ATAC Carbon
The tune stuff is spec'ed at: www.tune.de
Downgrade to a "lesser" spec, e.g. Tune Standardlaufräder leicht and Shimano XT, Time ATAC, you are still building an excellent bike.
Hope this helps, but perhaps i've caused more confusion, sorry if this is the case (;->)