Many thanks, andypugh! I have struggled to find a work around and the only thing that I have changed (to cut the best part so far) is breaking the large file in to 3 smaller ones. This helped in several of the areas, but in bobcad when using "profile" (used just to cut around a shape, no pocket removal) you must have studied the geometry to know with complete and total confidence the tool diameter plus the "finish cut allowance" will fit or the tool will cut adjacent material, referred to as "part avoidance", who would of knew. Having not to known what to expect from bobcad, I was at a disadvantage, they are not to forth coming about the shortcomings. While in bobcad there is a way to save 1 or a few operations, at a time, as a separate file, to memory stick to linuxcnc machine, so it is possible, but think about managing the tweaks. When you have a "pocket to cut" there seems to be a lot of time when the tool cuts air (I am aware there is a way to edit the gcode file) goes over an area already cut or long rapid travel, not as efficient as I would of thought, in addition, the cutter overlap is recommended "max" 50%. I welcome your thoughts. I have thought how I would approach a project like this in the future.
many thanks