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I went with using the z-axis as this is closer to DH notation which the whole calibration is heavily based on. I was not aware, that this would be a problem with IkFast, though.
Personally, I have never used IkFast directly, as I use trac_ik in most cases, so I cannot say for sure, which requirements it has in regards to the URDF.
Is there anyway to put the calibration data into the melodic-devel urdf or how to change the fmauch urdf to use the y axis as the axis of rotation for the joints?
I guess the second option would be easier to implement. For this, you'll "simply" have to rearrange everything correctly. However, I would suggest to do it on the melodic-devel-staging branch instead of on my fork, as there is only one xacro file left and my fork will die as soon as we have a working MoveIt! configuration inside melodic-devel-staging.
Because I suspect the different axis of rotation for the joints is the reason causing one can generate the IkFast plugin and the other cannot.
I would try to confirm that guess before diving into that work.
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