I have two things to help me mill short and odd pieces. First I made two movable bunks that fit between the rails. This allows me to support a piece that is long enough to clamp at each end but with the clamps laid over so the piece is only lying over one of the bunks on the mill. They're ugly, made from some angle iron and pieces from a elliptical that a friend gave me, but they work.
For really short pieces I have made a wooden table that fits tightly over two bunks. I can screw and/or clamp an irregular piece (such as a crotch) to this to hold it securely. The picture below shows a cottonwood crotch on the table. If you look closely you can see a deck screw at the lower left hand corner of the picture - this is holding the crotch to the table.
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