One good diagnostic for ammonia is falling pH while adding chlorine because oxidizing ammonia is acidic.
2NH4+ + 3OCl- --> N2 + 3H2O + 2H+ +3Cl-
When adding 12.5% sodium hypochlorite (liquid chlorine) to a pool to oxidize ammonia, every gallon of liquid chlorine will create the equivalent of 15 ounces of 31.45% hydrochloric acid.
Hydrogen sulfide will be oxidized to sulfur and sulfate. Sulfur will filter out and the sulfates will stay in the water.
The pen pH should not be effected by the FC. The ammonia elimination process increases your pH if I remember right -- Matt would know the chemistry better than I -----
I do not see why adding borax would bother. But hold off if your pH pen is showing higher pH. Add if FC under 10, your drop test should work.
I'm following this thread just for the learning. If I'm reading the above comment by James correctly, the ammonia elimination process is going to drive pH further downward, so you'll have to do something to correct it as you battle the ammonia further...