Today I have also noticed that two out of the four koi are scratching
themselves on the pump and plant baskets.

Parasites most likely.......

Possibly, but nitrites can also cause flashing/scratching.

Here are my questions,
Are there any other strategies to reduce the nitrite levels other than
being patient? Enough bacteria has been added.... I used this really
expensive "Microbial Lift" stuff from the fish shop. The guy there
said I was doing everything right in the meantime.

You should put some salt in so the nitrite doesn't cause brown blood
disease. About 1 lb of kosher salt (no anti-caking additives or iodine)
should do it. This will also ease the flashing (if due to nitrite). ~ jan
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See my ponds and filter design:
www.jjspond.us

~Keep 'em Wet!~
Tri-Cities WA Zone 7a
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