Hi,
First, you should have painted on one coat of ferric nitrate, let dry and blushed with heat thoroughly to see the result before putting on a second coat and blushing a second time. I have successfully touched up ferric nitrate staining after a single coat of finish. Lightly sand the area with 320 grit and apply the ferric nitrate, let dry and blush. You may bubble some finish but it can be easily wiped off. However, I am not sure how well that will work over a large area of stock and you may have trouble blending it with the rest of the stock. Stains such as Homer Dangler's that are alcohol based can be useful here because they will penetrate a thin finish. Also consider tinting the finish with Transtint dyes or stains such as Laurel Mtn Forge that are oil soluble.
dave