The Alli is computerized trans that is commanded to shift after certain parameters are met. Speed sensors, throttle position and such. When a fuel filter is restricted the throttle position will be different because it will take more to achieve the same speed and the resulting output speed will not meet the throttle angle according to the existing programming. When this happens the TCM thinks you are in partial detent or quasi passing gear and won't give a shift command till the proper output speed is attained which isn't going to happen with lack of fuel. Plain and simple; TCM just doesn't know what to do with all the wrong signals coming in. Hope this helps.