Linnie,
Trying to remove a heavy buildup of algae is impossible, and if you kill it in place, as you did, it may very well lead to clogging problems. It is best to not allow the algae to grow in the first place.
A periodic flushing with Physan or a one-ounce-per-gallon bleach solution will keep it at bay.
If you do get a slight buildup, just repot (any time - s/h to s/h does not stress a plant), stick the algaed pots in the diswasher (when my wife isn't looking), and continue on.
I also have to question if the root problems might not have been the old roots anyway? If that's the case, it's understandable and to be expected.
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