Go into your TTS and under tuning constants and change primary ratio setting. (Example if you are at 1.353 change to 1.330) it may fix both those problems.
TTS MasterTune Technical Bulletin MT-TB2010-02
This problem can sometimes occur even when the correct gearing is selected.
This is because the late model 6-speeds use a helical gear for the VSS sensor pick-up.
The helical fear does not give as good a signal as the older straight -cut gear-resulting in missed pulses.
This is compensated for by adjusting the primary ratio downward a bit.
This adjustment will not affect the speedometer calibration.
To fix the problem, the primary gear ratio setting in Constants needs to be reduced slightly.
For example, if the setting is currently 1.353 change the setting to 1.330 and check if the problem is solved.
In some cases it may be necessary to reduce the setting a bit more.