two thoughts come to mind. Copper and Iron. What type of algecide did you put in? If it was copper based and you shocked the pool it is possible that it might have colored the water green. You are using well water with a known iron content. Shocking could cause this water to turn yellowish to brownish.
Yellow and green make yellowish green color. Your low pH is perfect for any metals in your pool to stay in solution and not precipitate out as a stain. The oxidizing action of the shock could then cause them to form colored compounds in the water. I am not saying that this is what happened but it certainly is a possible explanation. The Bioguard Pool Magnet is a phosphonic acid derivative sequestering agent. It is possible that you did not have enough, expecially if the algecide that you added was copper based. It does not REMOVE the metals. It only makes them less likely to precipitate out as stain by keeping them in solution and the effect does wear off in time ( which is why it is necessary to continually redose). I believe it is still possible for them to be oxidized by very high shock levels (Someone with more experience please check me on this last statement....I have heard this as 'pool store info")