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I'm not sure exactly how simplify3d works but the "worms" phenomenon you described sounds like what normally happens when a a model is sliced for fdm. if you can, try lowering your layer height that may fix the issue. if you still have missing parts its probably due to the software determining that the parts are too thin to print at your resolution so it ignores them. i have doubts that even high tier fdm printers could handle these due to the large layer heights and support requirements.
(see attached photos of sliced model "worm" issue )