New Circuit Help Please - Feeding 2-gang receptacle boxes with MC 12/4
You gotta keep em separated!
You need to keep the neutrals separated throughout the circuit for a couple of reasons.  First off, if you want to put GFCI on this, the GFCI will tell you if you cross or join the neutrals by stubbornly refusing to stay un-tripped, so keeping them separated is a good policy that way.  More importantly, though, neutrals rely on being protected by the overcurrent devices of their partner hot wires, as they don't have fuses or overcurrent breakers of their own.  As a result, if you tie the neutrals together, and one of them opens, you'll potentially put 40A down a 12AWG wire, which is going to get rather toasty and melty...
And yes, you have the wrong cable for the job
While reidentifying neutrals to hots in a cable works, you can't take a wire smaller than 4AWG that's not white, grey, or striped with one of those two colors and legally use it as a neutral.  To be fair, if one was working under significant duress, tape-flagging a hot to a neutral is by no means the worst thing you can do, but it sounds like you'll have to order in some 12/2/2 MC and do this over.