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Because the Micro Swiss hot end is all metal, it requires a higher temperature to allow the heat to travel all the way to the junction between the hotend and the coolend. its usually about an extra 10C. the thermal paste is very important, as well as the adjustment in the aluminum block. if that is not right then the cool end can either be too hot, or it can rob heat from the hot end. both of these can cause clogs. so be pretty precise with the height adjustment in the aluminum block. Also the retraction being less than 2 mm makes a big difference as well as more than tat can cause the hot filament to retract into the cool end and causing a clog.

I had all these same problems until I really took the time to make sure I followed the instructions very carefully.