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Hi I am experiencing shiftshock in my 2005 Mitsubishi Lancer since the battery went flat, battery is fully charged now.

This is a common occurance after the battery has been disconnected, but it usually re-learns the shift pattern within a fairly short timeframe. If it persists, try disconnecting the battery again to wipe the memory, then take the car for a gentle drive to get the shift patterns back in synch.
One way or another, it should come right with a decent drive.