My situation was very similar to yours. At around 1 1/2 months she began straining and having a very difficult time making a bowel movement - she could be up for 3 hours at a time, straining and pushing, a lot of tears, and no result. We too went to a great GI. I was breastfeeding, but the docs made me try to stop for a little bit and try a formula to see if it was something I might be eating that she had a issue with (but I kept pumping). We tried Enfamil Lipil and Nutramagin. The first had no change, the second made her worse and she vomited it up.
So, I went back to breastfeeding. I have now eliminated:dairy, wheat, soy, gassy veggies, raw nuts and most glutens. The one thing that really seemed to make a difference was the nuts - though, we never saw the full change we wanted.
We put our poor little girl through a barium enema xray which came out negative.
The GI suggested a probiotic, Florastor which seemed to work some. Again, not completely.
She would go days in great discomfort - it wasn't that she just wasn't going, at this point (she was 4 months or so) they may not go for up to 7 days, but she was terribly uncomfortable, so this didn't seem normal.
So, I guess, I'm not giving you much of a quick answer, but, some of these things eased her discomfort, and I think time was the best, her little digestive system has been maturing.
At times when she was really uncomfortable, the GI had us use 1/2 of an infant glycerin suppository. We had to resort to that several times, and after we caused some movement down there, she seemed to have it a little easier on her own. So, I'm not sure how you feel about that.
One note, she was getting better, and then somewhere around 2 1/2 months she got her vaccinations and it set her right back to where she started, so be sure to check with the GI and pedi to make sure they think it's okay to go ahead with these as scheduled. (we had even split them, but the very night, her issues came back big time). A doc in my family thinks it is just that this was her weak spot, and the vaccs, set her back a bit.
Also, with regards to the breastmilk. My milk supply went down after I had to pump for so long while trying the formula, but, it's come back up, I spent a few days feeding her every two hours, and also took the "more milk plus" tincture (you can get it at whole foods or the pump station). Sometimes at the end of the day, it's a little low, but, I can bottle feed her some that I pump in the night.
Feel free to email me if you have any questions.
All the best,
roxane