Does the 060 daughterboard come with CPU, or without ?
It depends. Mike is trying to get some from China but so far all of them have turned out to be fakes.
is it possible in the future any solution between the Natami's 68050 and your daughterboard ?
(because the stock of rev6-060 not too much, and supply comes with lot of risks)
Yes, there are plans to create another daughterboard with a bigger FPGA which could act as high-performance CPU. The question remains: who will make the CPU core?
Did you use any cooling solution for 060 at 106 Mhz
Yes, small heatsink and small fan. At 100 MHz the CPU is able to run without active cooling.