Great thanks for the extra info - you might shift one to the corner the senior cat is using just to see if that helps.
You might try Feliway Cat appeasing pheromone to calm things down between the two of them. You can read about this here and it comes as a diffuser, and a spray.
http://www.catfeliway.com/feliway.html
You may find Cat Attract litter works
http://www.preciouscat.com/precious-attract-p-5.html
Lots more ideas on this page
http://www.tallyville.com/litterboxhelp.html
And if you can you might make one of the boxes more private so that the older cat cannot be pounced on by using it - maybe a covered box with a hole in the roof for entry like this one
http://www.petco.com/product/14467/Clevercat-Top-Entry-Litterbox.aspx
But if your vet has not seen the older cat and has not done a fecal exam to check to see if the kitten 'shared' any parasites with her then you might want to have a check up and a fecal test done.
One more thing - cats often indulge in very rough play that can look like a fight and then race through the house or quit and wash themselves. Make sure the fights are really fights.
Hope this helps you!
Cat Health, Behavior, Care Expert
30+ years cat owner, rescue, breeding, study of behavior & health care