While I dont have an Excel like yours, I can tell you that having the transmission be a couple of liters low on fluid will not hurt it in any way - unless you drove it that way for a long distance; like hundreds of kilometers. Having it filled up should be checked out though. It takes a little driving or running the shift lever through the gears to get the air bubbles out of the transmission, if its been very low. So be sure to check the trans fluid again, with the engine idling and in Park. It may still need more fluid.
And while I cant imagine anything could be wrong with an axle shaft that would cause your symptoms - I CAN believe that something else was disturbed by the process of replacing the axle, and needs to be fixed. Im think of a connector being loose somewhere (I think your transmission has electronic controls), or the trans isnt getting a signal as to the position of the gas pedal. This would involve some connection to the car's computer, or at least its transmission control module.