What are the real meanings of the many primitives we learn with the Heisig method? I refer to the primitives which are not stand-alone kanjis. (Or perhaps they are stand-alone kanji, just not part of the 3000 Heisig kanjis?)

Many times Heisig chose a meaning for those primitives which makes it easier to come up with mnemic stories, but there must be real, traditional meanings behind them.

Keep in mind that some of what Heisig calls primitives are not "real" elements, or at least not in the ones used as radicals in the tradition started by the Kangxi dictionary. However, I think this is what you're looking for: http://www.kanjiclinic.com/radicalnames.htm

It has the Japanese names for the radicals, as well as their English meaning