Yep, adding both baking soda and acid is counteracting. You may need some alkalinity in the mash due to the large amount of calcium added via the gypsum, but you shouldn’t have to add both the acid and baking soda. Add one or the other, not both. Try dialing back the acid totally and then dial back the baking soda until the pH is correct. If the pH is still too high after you’ve removed all the baking soda, then start adding the acid. Remember, in a hoppy beer, 5.4 is a good target.
Magnesium is not such a bad thing to have in brewing water. AHA members will see in the next issue of Zymurgy that Mg is typical in Bavarian waters and they make pretty good beers there…even malty ones. But their Mg level is typically below 20 ppm. I feel that adding a modest concentration of Mg in hoppy beers is very helpful to flavor. More importantly, adding epsom salt boosts sulfate without adding too much calcium. Although ale yeast are relatively tolerant of calcium, I do think we use a bit too much in some brewing. Calcium is certainly detrimental to lager yeasts and should be kept relatively low in most cases. The 50 ppm minimum calcium mantra does not apply to lagers.
By the way, the Supporter’s version of Bru’n Water automatically alerts the brewer when they are adding both an acid and an alkaline mineral to the mash.