I think it is great you have been able to pump and store enough for an additional 3 months! This means your son will get 6 months of breastmilk which is great. I know what a commitment pumping can be. And, I am sorry that you received a post that didn't attempt to answer your questions, but rather justs tells you to go back to breastfeeding. I am sure you know the benefits of breastmilk, especially given that you commited to pumping!
I have breastfed and exclusively pumped myself. I have also had a child on zantac. Be aware that the zantac they get is not baby zantac, but the same as what an adult receives, just a lower dose. Zantac can indeed have an effect on their bms. Also, since your son is probably getting around 1/5 formula, 4/5 breastmilk, my guess is that you aren't seeing fully how the baby will react on formula. Since the majority of his intake is still breastmilk, I would expect runnier bm's like breastfed babies.
Regarding formula, people often switch formula too soon, so you may want to wait a bit before doing that. However, in researching formula myself, I learned that Similac Sensitive is lactose free. It is very rare for babies to have lactose issues and it is in your breastmilk, so many peds don't recommend going with a formula without breastmilk. A couple of other ones to consider might be Nestle Good Start (it only has whey protiens, not casein and they are partially broken down so they are easier to digest) or Enfamil Gentlease (also partially broken with only 1/5 less lactose than normal). When/if I introduce formula, I also plan on starting with a bottle a day. I have heard some do 1/2 formula and 1/2 breastmilk, but the only bad thing about that is that if the baby doesn't finish the bottle, you are going to have to throw out breastmilk.
Lastly, I know that breastfed babies initially have way more bowel movements than formula fed babies, however, later on this changes where breastfed babies can actually go a day or two without a bm. So, it could be that your baby is getting to that stage.
Either way, I agree with another post that said you know when you should call a doctor. Follow your instinct!