The Allison 1, 2, 3 and 4000 can be reprogrammed from five to six speed. HOWEVER, most applications that are five speed are that way because of driveline limitations. You must make sure your driveline can handle the extra speed before doing this modification. Dana has an excellent driveline calculation program called Dana Expert that is available on the web. A 2500 RPM engine with a .66 overdrive will cause the propshaft(s) to turn at about 3800 RPM. Unless your driveline size, angularity and offsets are engineered for this RPM, you risk vibration and potentially dangerous consequences.
The 3000 is produced as a seven speed, but that is done with the addition of one clutch (C6) and its planetary. The 4000 is available as a seven speed for use in stationary equipment mostly.
I don't remember offhand why the aftermarket companies require the valve body be changed on the 1000 and 2000.
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