Wish I had some magic words to throw in here about the freckles, but I'm at a loss. I can't see where baking soda should be able to make any sort of reaction, either. Frustrating and puzzling. If you scrub on them with oiled steel wool do they diminish at all? Below are some tips that I have and will be following.
Not knowing the nature of your air compressor I'd avoid using it for this type of work. Any contaminant in the air or tank (moisture, oil, rust particles) get blasted onto your project. Use a heat gun to dry parts as soon as you pull them from the water, paying particular attention to any holes, threads, crevices to prevent streaking.
After each carding or other handling activity swish parts in acetone and dry with the heat gun before subsequent bluing steps. Keep wire brushes and steel wool washed similarly. Even avoid touching the gloves you wear at any point other than the cuff.
Get a box of nitrile gloves ajnd change them frequently.
Use a clean shop towel every time you lay parts in process on the table or work surface. Use a sheet of something under it to prevent contamination from anything residing on your workbench.
Put a small amount of bluing solution into a small glass cup to avoid contaminating the bottle. It only takes about a teaspoon to do an application to a pistol. Discard this after each acid step.
I used the American Classic from Brownells because I figured it was the same as a name brand. It should be essentially nitric acid, hydrochloric acid, iron powder that's been reacted in the mix, and water. I wasn't going to spend 3x the price for the same product in a different bottle.
When I do my final boil I will add about 2-4 tbsp baking soda after the parts have boiled for 20 min., then boil another 10 min before rinsing in heated, distilled water and again drying with a heat gun. As soon as this is done it gets soaked liberally in wd40 and held as wet as possible like this (immersed or wrapped in soaked shop towels) and held for a day before wiping it down.
After the wd40 it'll be warmed again with the heat gun and liberally coated/rubbed/soaked in boiled linseed oil and again wrapped in oil soaked towels for a day.
Finally some more gentle heating and a thorough rubdown should finish it and make it ready for any typical gun protectant and reassembly.