If the problem started when you had the leak and added fluid, I would try using the correct fluid. The Amsoil Universal ATF is claimed to work for just about every transmission by Amsoil, but it doesn't actually meet the LT71141 spec, it is just claimed to be an acceptable alternate by Amsoil. That specific fluid was developed with specific frictional characteristics to smooth shifts, and rough shifting is the problem you are experiencing.

It would be cheaper than just about any other fix, and might be worth trying first.

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2007 X3 3.0si, 6 MT, Premium, White

Retired:
2008 535i, 6 MT, M Sport, Premium, Space Grey
2003 X5 3.0 Steptronic, Premium, Titanium Silver
2002 325xi 5 MT, Steel Grey
2004 Z4 3.0 Premium, Sport, SMG, Maldives Blue