If that's your only concern I think you have a couple options:

I think the V3 Head/Body morph pack comes with a .CR2 that is all pre-Injected.  It's the V3 SAE figure.

If not, Load/install the V3 Morphs into their own Runtime, and switch to it.  Then load a V3 .CR2 with all of the Head and Body morphs.  Once this is done if save the .CR2, and .PZ3, you wo'nt need that runtime again.

Then INJ files will just set morphs for you.  And you could use something like SVDL's Free Remove Morphs.py to clear out the MTs that were'nt reset(Are at zero.)

Hope this is better news!