When the spots were first noticed the water was a bit neglected:

Chlorine (SWG not working) was at 0 (not sure for how long)
Stabilizer was at 30
Phospates were at 1000
ph was ok

Following the pool store advice (before finding this forum), I got the SWG fixed and boosted for 72 hrs. Added 4 lbs of stabilizer, 4 capfuls of Phosfree, and half a bottle of Black Algaecide (not all at the same time). I also began scrubbing the spots twice a day for about a week with a wire brush.

Now, as a result, have the following numbers:

Chlorine is maxing out on my tester at 5, and has been there for a few days now.
PH is perfect, only demanding a little acid to keep in check
Stablizier is at 100
PHospates are at 0

The spots look 100% better than they did, but they are still visible to me. More greyish than black now, but still remnants in the little craters they seem to have formed. I continue to scrub by hand while diving, but just cant seem to get them all out.

I assume this was black algae spots, Is there something more I can do? Should I have not added the copper algaecide? What next? I really want to get rid of all of it. Any suggestions would be great.