Allison Transmission Questions Hi Captain, So sorry I did not return your call or answer sooner, very very busy at work (good thing). The cooler flush is done at the end but before you start up you disconnect line and then have someone start it up. I hope this is how they did it. They must have done it correct. What you are probably experiencing is the clean fluid will sometime make the transmission shift different. My suggestion is to take to an Allison Distributer (not dealer) and have them do what is called unadapt shiftpoints and then set up for fast adapt. This will blank out computer shift quality and then reset them during test drive. It usually will take care of rough shifting. You might also have them check the output speed tonewheel. Sometimes the pin that holds this wheel wears into the wheel and makes it loose causing erratic intermittent shifts. Good luck and let me know how things go. Thanks and have a great day!