After reading the replies I'm realizing I need to add some more background info.
After you guys got me pointed in the right direction with applying AF, I neutralized a scrap and it washed out slightly. No issues as it came back to the desired tone when oil was applied.
I then went to a maple stock which was sanded down to 400 grit and whiskered between sandings. After applying and warming the AF, the stock was a little darker than desired but I figured it would rub back a bit when neutralized.
Following neutralizing with baking soda and distilled water, the stock was left to dry and came out considerably lighter and uneven in places. Particularly around sharp edges and more rounded areas (edge of lower butt, cheekpiece edge, wrist, lower forearm, etc. Some of these areas show almost no color.
I initially assumed it was due to being too aggressive when removing the baking soda mixture (as Dan mentioned) or possibly my AF solution being too weak for this piece of maple.
Some observations; 1. Before neutralizing, I tried to apply a second treatment of AF as some mentioned they apply several coats. The maple wouldn't absorb anymore AF, it appeared to only streak across the stock and not penetrate. 2. After it was neutralized and dried out, I noticed almost none of the grain was raised as I'd expected to see. 3. Following the neutralization of my test scraps, I found the penetration to be deep enough that the blush remained dark and even across the entire piece.
Is it okay to apply another, possibly stronger application of AF? What's a good estimate of the time it takes for the solution to neutralize the acid?
Thanks for the help so far.