Boards like that Up^2 sound really good to me. But like others such as the Udoo x86 they are still in preorder or just very expensive.
Regarding LinuxCNC on the Pi3: my SD image contains too much 'experimental stuff' to be able to safely hand it over. My Pi is used to all that misuse, but yours probably burst in flames :laugh:
However, I can try to build .deb packages for the kernel. Never did it before, so no idea how complicated it is.
In the meantime you can get a working realtime kernel from
www.frank-durr.de/?p=203
That kernel works fine, it only lacks support for the Pi3 WiFi. This is why I took the Pi foundation kernel sources and patched it with the closest matching PREEMPT_RT patch. Building and installing the Pi kernel is described here:
www.raspberrypi.org/documentation/linux/kernel/building.md
Building LinuxCNC is described here:
linuxcnc.org/docs/devel/html/code/building-linuxcnc.html
Once you get to the ./configure step, make sure to use ./configure --with-realtime=uspace.