Dissimilar wear on the two pads is normal. Depending on the rpm and the related position of the actuator one of the pads gets more pressure than the other. I think depending on what rpm range you use the car the most determines which pad will wear more.
As long as you don`t remove the tensioners on the other bank and everything is timed and obviosly you don`t remove the IMS flange, it`s safe to rotate the crankshaft if you removed the camshafts. Just make sure you hold the chain tight so it won`t get jammed in the crankcase.
The colored links need to be set only at assembly. If you want to check timing you need to look at the positions of the camshaft marks relative to TDC.
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