I was about to suggest leg curls. People will tell you oh leg curls are for pussies and they arnt functional blah blah blah but I like lying leg curls and they have been a staple on my hamstring day since I started a split routine. I get a better contraction that RDL's or hypers and they also hit calves hard. Granted I get a better stretch with a romanian deadlift and I can use more weight but by the sounds of it you cant do romanian deadlifts or hypers so leg curls sound like a good alternative for you.
Why not do this for your lower body day
Squats
Calves
Leg Curls
Abs
just do more sets than usual for the squats and leg curls since they are all your doing...
that is probably what I would do in your situation anyway. And depending on how you squat you may feel like leg extensions would benefit you, but if you primarily squat with your quads then you might not feel the need for them.