I believe I fixed the bug! It was a problem with starting orig_indices at 2 instead of 1 in model_v2.f90. I am surpised they didn't have this problem before, actually. I suppose they might have, it's just that Paul over wrote the models every so often so maybe that fixed the issue??? I do not know at the moment, but it is something to think about.
Forgot to change the saving preferences to not save every single step.
I also am going to save the mrot(1) model every time I save the m model in rmc.