If I was low on the day I took B12, what connection are you seeing between RBC and the symptoms I was having? I'm not seeing it. Maybe there is more to iron than I realise!
The low iron can cause lower amounts of RBC (and blood volume?). When your RBC drops, there's less for even normal amounts of iron to bind to - and if you increase RBC and/or blood volume without a corresponding increase in iron (needed to bind oxygen), your body really might not like that.
And once RBC or blood volume is lost, it takes some time to build them back up, combined with taking iron to make sure they're nice and happy RBCs. Since you don't consistently need iron and sometimes stop taking it, there's probably times when levels of it keep going down, maybe while your RBCs are trying to go up, etc.
Basically there's a cycle where RBCs drop, which causes iron to drop, which causes RBC production to stay low. And B12 might be trying to force more RBC production, even if you don't have enough iron to keep the extra RBCs happy. So iron and B12 are both capable of interacting with your RBCs quite a bit, and a dysfunction in iron might make it difficult for your RBCs to interact with B12 properly.
Or there might be something else entirely going on
I think finding the cause of your iron deficiency would be a great place to start, though I have no idea how that's done. If you've got intestinal bleeding or something, then it would certainly be good to have that treated!
Another possibility is that you'll need iron supplementation when starting up B12 supplementation, so that the iron is available for any increase in RBCs cause by the B12.