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I recently got a small 3020 CNC and have done some headstock inlays but I'd like to do some fretboard inlays next. I plan on excluding the machine to 34" down the line, but for now it's not long enough to radius fretboards.

Is it better to radius the fretboard by had first or to inlay and then radius? My materials are ~ .060-.062. My radius is 16'.

Also until I expand the machine does anyone see any problems with doing the half the fretboard, re-positioning and re-zeroing the machine and then cutting the other half?

Position the fret board on a diagonal. It might fit.
I have only built about twelve necks but I always radius the board and then inlay, not saying that is the right way however, just how I do it. Got to be carefull not to sand thru the edges if the inlay piece is wide, like with a shark tooth pattern.

WARNING: I have only done one fretboard on my CNC, so I am no expert! Take my advice at your own risk!

I radiused my FB first because I was concerned that the ball mill I used for radiusing would shatter the shell material if I inlaid it first and then cut both the wood and shell with the ball mill in the radiusing operation. Maybe I was paranoid.

If the FB will not fit diagonally on your CNC bed, repositioning it should work. However, you'll need a method to ensure that things line up properly when you reposition. I found that putting positioning holes on the back of the fretboard (and corresponding holes in my spoil board) was critical to keeping everying aligned, as I had to remove the fretboard several times between operations. For example, after I radiused and cut the inlay channels, I removed the board so I couid install the inlay before cutting the fret slots. The positioning holes allowed me to put the FB back in exactly the same position so that the fret slots would be positioned correctly on the board. You should be able to cut a set of positioning holes that will ensure things line up properly when repositioning.