all you did was the valvebody right? If you go in manual mode does your gear position indicator work right? The only things that should effect the synchro rev are if the gear position sensor is out, or if there is an issue with the speed signals or in uprev flash. Reflashing, resetting the ecu, maybe putting the stock tune back on just to shift it a couple times and see if synchro rev comes back would be a good couple of first steps. the ecu drops line pressure at low loads so it is not going to shift hard under full throttle. you could always have your tuner up the low load parts of the torque map if you want hard shifts all the time but you shouldn't need lightning shifts cruising around town.
Edit: are you getting any codes?
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