The marking on OEM Dana pinions is how much the pinion deviates from a standard reference point (in other words, if your old pinion has -1 on it, and the new one has +2 on it, you'd subtract .003 from your shim stack thickness to put it in the same position relative to the ring gear). Unfortunately most aftermarket gears lack such markings, so you'll have to use conventional trial & error methods to set those up.
Did the shim fall out after you took the pinion race out, or before? If it came out after the race, it's possible it's a pinion depth shim (which on Dana axles, goes under the inner (main) bearing race). Ford axles normally have them under the pinion bearing cone though, so I'm not sure that's what it is.
IMO, if you're not sure how to check your shim thicknesses, you may be over your head on this.
Gear setup is not something to take lightly, there are numerous tolerances that if not correct (even within a couple thousandths), the gears may fail without provocation. You might want to take it into a shop and have them do the setup on it (or maybe if you have a buddy that's familiar with it, you can seek some help on it from him).