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My car has been reflashed with cobb, Ypipe, exhaust. No problem in trans after that reflash.

Last week I install the injectors, fuel pumps, intake and downpipe and reflash the ecu.

The transmission is not smooth now (upshift & downshift), is the cobb ecu reflash affect the trans also? My tuner said he did not reflash the TCM, only the ecu.
It's not jerky before the ecu reflash when I install of the injectors, fuel pumps, intake and downpipe.
 
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