From my point of view the first suggestion would be GoodMorning's, which can be done seated in some cases. Should see improvement in the lower back, hips and hams when handling respectable weight in the squat. Can work up to some very heavy weight on the GM'ing after awhile. The stronger the low back becomes, the stronger the squat becomes. Even reducing the threat of injury in that exercise. Might also pay attention to the abs and train them with serious intent. Like heavy, in a 5 to 7 rep mode. Abs and lower back work together in most all exercises. Most greatly in squatting or DL'ing.
Second Romanian DL's. SLDL are a very similar to RD's if the lower back is kept somewhat flat and not allowed to stretch or round out too much. Hypers, as offered by Dy, are a excellent exercise, used in most rehab centers in the US. Other very advanced lower back devises in more select training gyms, not for the average lifter.
Really no need to go much lower (2 to 3 inches...for any body structure) than the 90 degree plain, though there a a few pro's & con's on this. Going ass to the grass does sound kind of cool and all that, but no need to. Wo0o gives good advice about front squats, a favorite for me. Though some guy's will round the back in the lowest position if the weight is too heavy. Either regular or front squats it's all about complete control, balance and position. Good Luck.
