Design and content
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By joining the two mufflers, the crossover tube reduces the resistance the exhaust gases must overcome, and allows the exhaust already moving down the pipe to suck the exhaust gases out of the cylinder whose valve has just opened. Both of these are Good Things. This is why the best performing aftermarket pipes for any type of motorcycle join the exhaust tubes.
Removing it by only replacing the stock headers will cause a power loss.
Porker Pipes and Drags
On the question of installing open drag pipes:
"unless you have had some engine modifications to allow for it, you _will_ be down on power (maybe more power than the stock, but less than if you used "tuned" pipes). Engines are built to compensate for a certain amount of back-pressure (i.e. the valves opening a little earlier), and if you remove the backpressure, the valves will be opening too early, letting some still-burning fuel into the headers. ... because of this, you can suffer (in extreme cases) from burnt exhaust valves if you hammer it too hard..." -- Mike Kelly
To calculate the proper length of drag pipes the following formula was pulled from The Design and Tuning of Competition Engines by Philip H. Smith
"The pipe diameter internally is based on the dimensions of the valve throughway. This formula will do no more than ensure that the pipe is of adequate length to give a good pressure-wave action, particularly at higher speeds; it must be emphasized that there is no formula in existence which enables a system to be "designed" completely on paper, experiment being essential for the absolutely final result." [pgs 326-327 from the same above]
The WB catalog suggests slip-on mufflers or a Supertrapp 2-into-1 pipe with 18 discs and a racing open end cap over their own Porker Pipes for performance applications.
The following is a list of replacement exhaust systems, listed in order of performance as rated by r.m.h conventional wisdom. It is important to note that there is not a great deal separating the four and that by far the slip-ons are considered the best value.
Bub Bad Dogs -- I used these on my Dyna and really liked them. My dynometer tests didn't show near the HP gains advertised but what else is new? One unexpected benifit is the greatly reduced vibration due to the reduced weight.
Python II -- Good mid and high range, though down on torque at low RPM
Thunderheader -- Quality control problems reported, tunable
SE Slip-on mufflers -- A Dyna was recently "King of the Hill" for two days at the Sturgis dyno with 116hp using SE slip-on mufflers.
V&H Pro Pipes -- Tunable