I was about to ask the same thing, if you all were using blue glass cleaner or what. What kind of mixture, more or less, are you using of household ammonia?
I have been using lye for years. It does eat my fingerprints off, but it works, and does turn the color a bit more red. I rinse the stock off afterwards with the garden hose. By the time I'm done staining, there is NO more grain raising anyway, so that hasn't been a concern.
Many years ago, I did two modern gun stocks (one birch, one beech) with A.F. and didn't neutralize. Within 5 years the birch was almost black, and the beech was VERY dark red.