New painted turtle disharmony

Question
I have kept 3 natively acquired (? eastern) painted turtles together in a 40 gal breeder aquarium for several years.  The largest is Yertle, a female (6" carapace), and the other two are Hutch (male, 4") and Morty (female, 4").  My gender recognition is based on my understanding that males have longer claws and a longer tail.  Correct?  Also, last winter I witnessed actual intercourse between Hutch and Yertle.  At any rate, the 3 have communed very well in their tank for many years, often stacked up together on the rocks under the warmth of the basking light.  However, things drastically changed this past June after a change was made in their habitat and while I was away for 2 weeks.  First, I had been recommended to install those suction-cupped, floating "turtle docks" by my local pet store instead using my traditional rocks---to decrease algae growth and improve ease of cleaning the tank.  These were installed by my friend and temporary pet-sitter shortly after I left town.  I then learned that the turtles were having difficulty getting onto the docks and that they could easily knock each other off while attempting to climb on.  Upon my return nearly 2 weeks later, I immediately noticed that Yertle's right eye was not visible and was covered by whitish, shreds of tissue.  There were also areas along her neck, legs, and back end appearing the same.  I panicked and brought her to our local vet who sees exotics and he pointed out that her nails were worn almost completely down and that most certainly she had been assaulted by her tank-mate(s).  Needless to say, my friend felt horrible about not recognizing the warning signs of domestic violence.  I followed his directions of setting up a separate, small nursing tank for Yertle, and giving her brief, daily salt water soaks along with applying vitamin A and E gels to her eye and other wounds.  Amazingly, her wounds have since healed, her eye is visible and functioning (from my perspective), and by looking at her now you would never know what had happened.  EXCEPT, I have not been able to successfully re-introduce them.  The floating docks are long gone and the large tank once again has a nice rock cave with basking area above.  The small "nursing" tank has a similar set up.  The 2 smaller turtles (Hutch & Morty) get along just fine, regardless of which tank they are in. I have tried placing all 3 together or just the 2 females together in the large tank (assuming the Hutch-Yertle combo was the problem).  Immediately, the smaller turtles begin chasing Yertle, relentlessly approaching and cornering her.  It seems worse when all 3 are together but also occurs with just the 2 females together.  At first I thought they (Hutch & Morty) were just curious and that perhaps they don't really "remember" Yertle---hence all the attention.  However, on several occasions, I've witnessed some biting, and the smaller female (Morty) has even clamped down on Yertle's foot and I have had to free her.  Needless to say I don't leave them together unsupervised.  Is this all normal turtle behavior?  Are they just getting re-acquainted, and should I let them "work it out"?  I am concerned about Yertle's safety, given the history.  Today I had the notion to try having Yertle & Hutch together  (Morty alone in the small tank) and although there is certainly some curiosity, it appears mainly mutual and I have yet to witness any actual violence (they've only been together a couple hours).  I am hoping you might be able to shed some light on these turtle dynamics.  Things were going along so smoothly until the change in habitat (since rectified), but the changes in behavior and conflict clearly remain an issue.  Could the problem be the younger female (Morty) now competing with Yertle?  All along I assumed the problem was with Hutch (the male) having assaulted Yertle, or that he and Morty had ganged up on her.  If possible, I would love to find a way for all 3 to live harmoniously once again. I appreciate any insight you may offer.
Thanks,
Shelly

Answer
I was a bit amused that you are calling a 40 gallon tank 'big'. The guideline for tank sizing is about 10 gallons of water per inch of shell length. With 14 linear inches of turtle shell, you should have these guys in a least 140 gallons of water.

This is important because aggression is a classic sign of over-crowding. We often find that turtles can live together peacefully in very over-crowded conditions, then for reasons that often do not make sense, something causes them to 'snap'. We also often find that one turtle is more likely to be the bully than others and that the aggression continues until the space requirements are met.

Those dang suction-cup docks truly are pretty worthless for adult or near-adult turtles, not being anywhere strong enough for them. On the other hand, rocks tend to cause a lot of problems as well. I prefer driftwood or similar materials.

You can check out http://www.austinsturtlepage.com and the sister forum http://www.turtleforum.com and see if they have any other ideas, but it is my experience that the only real option you have is a larger habitat.