I drive an Octavia Mark II (2012, 1.6 automatic) I have issues with the valve body on the transmission  and initially wanted to replace it though expensive. My mechanic tells me its better i opt for a second hand  gear box and that the Golf V gear box will fit without problems.

Opinions are most wellcome and will be appreciated.

As long as you will be able to transfer all the data from old to new gearbox then no problem!