I think LLLMeg had some excellent thoughts. Your situation is very puzzling. You've been doing everything right, yet your baby hasn't been gaining weight the way he should. The one thing that's just obvious to me is that whatever is going on, your milk isn't the problem. There's just no such thing as a mom who makes calorie-deficient milk. In fact, in a side-by-side comparison breastmilk generally averages slightly more calories than formula. Which is why, in your shoes, I would haul out the pump again and start pumping. 3 oz of breastmilk should be more calorie-dense than 3 oz of formula, and pumping out the supplements rather than getting them from a can will keep your supply equal to baby's needs.
I would also think about getting a professional scale, and doing your own weigh-feed-weigh tests at home. It's great that you did one (at the LC's office, I guess?), but one data point doesn't tell you much because milk intake is so variable. You want several days' worth of data before you draw conclusions about what your baby's average nursing intake is.
The final thing I would encourage you to do would be to see a different pediatrician- fresh eyes may see further!- and ask about additional testing for metabolic issues. There are a lot of metabolic diseases which get missed because they are rare, sometimes very rare, and that means they don't get included in the usual tests. I'd want to know what exactly your LO has been tested for thus far, and then discuss expanding the panel if necessary.