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I know your post is a little old, but i figured i would try to help. On the older 6.9 and 7.3 timing was set by a the injection pump and thick fuel can make it retard a little.
It sound like you have a PSD, witch i believe is timed by the electronic injectors, i guess as long as you have enough fuel pressure than it wouldn't hurt anything. I don't know much about powerstrokes.
WMO can cause problems, especially if you don't filter it very fine. You can't hurt by running a little at a time if your worried about it.
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1987 F250 XLT Lariat 
Regular Cab 2x4 6.9L 5-Speed
Homemade Propane Injection.
RUNS ON PURE WASTE MOTOR OIL!
No more diesel for me... 
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