I just brewed a stout last weekend. Unfortunately, I learned this lesson of steeping the dark grains after my LHBS milled all the grains together for me. What I did do was monitor the PH during the mash and then added 1/8th teaspoons of calcium carbonate to the mash as needed to keep the PH level close to 5.2-5.4. The beer is still fermenting but I did try to keep my dosing levels low so as not to "over adjust" a common problem I have read from beer judges that hate newbies adding so many PH adjusting chemicals to their beer that it ends up tasting like alka-seltzer.