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What you can try and do is to dis connect the both the battery cables and hold them together for more than one minute. Dis should dis charge the capacitors in the ECU module and wipe out the fault code. I do not think that there is a real problem with your car this might just be from the battery being dead.
We cleared the codes and it still shifts funny. Owner said it shifted fine before
Try a throttle reset.
Ok. That's what I was leaning towards as well will try it
It should do the trick.