I was wondering about low stomach acid, is this related to a lack of b12/iron in the system?

Yes, once methylation improves, you end up producing more stomach acid and bile salts.

For example, taurine forms one of your major bile salts. And taurine is a by-product of the methylation cycle.

And then also, Vitamin B6 is required for the production of histamine. And histamine stimulates the production of gastric acid. 

But when you have low Flavin Adenine Dinucleotide and Flavin Mononucleotide, you get a cellular B6 deficiency. Because Flavin Adenine Dinucleotide is required to activate B6.  

So then when you have low coenzymes, you also end up having low stomach acid down the line.