Update
Only two tanks running right now, 15-16 gallon has the shrimp, otos, and guppies, and 46 gallon (dad said it was a 55, but I measured before dosing meds and it's actually a 46) has mollies, platies and others. I had to delay treatment by a few days in order for more meds to arrive to have enough to treat both tanks. Treated both tanks with ndx (anti round worm) on August 6th, large water changes 24 hours later. No signs of improvement in the sickly fish, so suspect it's flatworms they were struggling with.
gdex (roundworm treatment) and 2000 (anti-bacterial) arrived and dosed on the 8th, both tanks treated. Three day course given, and the sickly looking female and fry perked up quickly, and look normal and healthy now, so seems to confirm it was roundworms making them struggle. Water tested on 12th and there was an ammonia spike, I suspect the antibacterial med killed a lot of beneficial bacteria and crashed the cycle. My tank only showed low levels, but it's heavily planted; the 46 gallon had much higher levels, large water changes done on both. My mistake in not testing the water during and immediately after treatment. Since treatment started, I have lost two otocinclus and a shrimp, and one fry - the one that had seemed the most badly affected before treatment started. One oto on the 7th, one on the 11th. I think the shrimp and perhaps one oto were due to ammonia spike, not necessarily the meds themselves. The other otocinclus might also be unconnected since it was before ammonia spike, my otos have been in hard water for nearly a year now
so it might well have been internal organ damage from mineral content, or it was from the NDX, but the other otos don't appear to be stuggling. The one that passed had seemed stressed the day before
My tank survived the ammonia spike pretty well since it's heavily planted, the 46 gallon more affected, but those fish all survived well and seemed unaffected. Large water changes and adding a big bunch of elodea had water parameters back to normal levels quickly.
Started second course of gdex and 2000 yesterday, monitoring water parameters more closely this time.
So I think despite not being able to identify what worm was causing this, the broad approach to treatment has worked, with fewer losses than I expected. Will complete second course of gdex and 2000 on the 17th, large water changes, then second dose of ndx on the 20th. Will do 3rd dose of ndx on the 3rd September, just to be on the safe side since I never want to go through this again, then I'll feel safe enough to move fish into new set ups after bleaching all equipment used again.