I have better results tracing the plans rather than cleaning up someone's PDF. If you trace and weld or meld your line segments you get a much cleaner cut with far less wasted time raising and lowering the cutter head.
I also like to do three passes. The first at etch depth to apply the special instructions, location marks, and parts designations if needed. I run the etch for every line. The second is the score depth, which is applied to all lines except the etch lines. The third is full cut depth, applied to full cut lines only. The gives me a very clean finish cut. It takes a little longer, but most of the time is hands off.