nick, a word to the wise. i know its tiresome to keep looking at the same problem, but if its throwing you a code (which it is) then you still have a problem and if it's not fixed you will be out a ride and posting "anyone have an E40D?"
if it was me i would put a trans temp sensor on and see how hot she gets when it starts shifting hard. everything shifts smooth when cold, thats why tranny stop leak and hard shifting lube is like honey.
also talk to the guys at the shop your going to if you have them do the filter and fluid, and see if there is a shift improver kit installed.
good luck man...im taking the easy way out for my E40D...its called Borg Warner.
I got tired of distributer gears stripping and coil packs burning out, so i bought a diesel.
Im getting tired of torque converters, now im getting a stick...see a trend?