Hi Marcus,
Theres no doubt that the YZ has the best overall package. In 2000 Kaw copied the same port shapes with minor changes to accomodate the KIPS valve. But the biggest mistake was to advance the port timing 1mm over the YZ. Yamaha hasn't struggled with reliability in the past 3 years. 1999 was probably the hottest model year 125 they ever made. But with an ignition map that was sensitive to good quality fuel, and a cylinder with narrow bridgework, hords or riders broke open their piggy banks to keep them running. But Yamaha responded to the reliability issue and improved the top end by widening the bridges, shrinking the ports, changing the head- stud pattern, and a rear port and piston pinning that should cure the reliability issues for good. The rear boost port is two narrow ports and the ring centering pin of the piston runs down the middle. Thats similar to Suzuki's design and something that I've been promoting on my 58mm pistons.
Centering the ring pin enables tuners new freedom in transfer port design. Now the rear transfer sets can be widened, re-angled, or whatever. This is common to the RM and YZ. Another thing common to these bikes is the exhaust valve design. It has two distinct functions, to reduce vary the effective stroke (distance from TDC to exhaust port opening) and the exhaust port velocity. The RM is more effective but Yamaha changed the size of the valve so when in the wide open position, the valve cleanly tucks up into the exhaust port roof, whereas the RM has a nasty sharp v-groove. While we're on that topic, the comments you make about the Kaw are clicking. The valves open at 8,000 rpm, if theres a dip in the torque curve on the dyno, its probably linked to the fact that the valve is in transition. The new KX KIPS valve is far more reliable that previous designs. Theres no more articulating flap that can break and shred the top end. Now theres 2 sliding plates, its a great idea but probably needs some tuning. I'll keep an eye on that and keep you all informed of what I find out. Regarding the porting, Kaw retarded the port timing over last years model and I'm sure all it needs is a little fiddling to suit any particular rider.
What happened to the Honda you might ask? They seemed to be on the right track last year, making significant changes to adapt their 10 year old street bike cylinder to a dirt bike. For 2002 it seems like the design team was torn over whether to make it torquey and rideable or pipey and orientated more for experts. So what they did was advance the port timing to be on par with a typical shifter kart or roadracer, then they strapped on a reed valve spacer and smaller area and longer exhaust manifold to try and get more low end. The problem is they don't work in sych. But I'm glad Honda made the manifolds available. For more low end on the 02 I'm turning down the base of the cylinder 1mm and recutting the head, stuffing the rear transfers and keeping the stock manifold. For more top end I'm grinding the upper corners of the exhaust port to allow for more blow-by past the outsides of the valves and using the 01 exhaust manifold. We did the low end mods to Rich Rohrich's 01CR125 and now his lap times are improving and he's more competitive in the tight sections like turns and whoops. Of course the R&D technicians would ask why a 5'5" 250 pound adult is riding a 125cc dirt bike when he's much better suited to velo bicycle racing or carrying safes up staircases.
The point is the manufacturers should stop trying to win the Dynojet Colored Line contest that appears in magazines every year, and start looking at the people who buy their bikes and asking them what they want. Maybe they should consider selling tuning kits that affect the powerband for a certain riding style or racing.