So does your lower back hurt after SLDLs in the morning or not until after squatting later on? Perhaps both? Also, what kind of pain? Is it the kind of pain that drops off about 10 mins after the offending exercise?
I find I get a sort of cramping pain for about 5 minutes or so after heavy deadlifts towards the end of the cycle (when I'm in the 5s). I squat before deadlifts and never get a problem from the squats. It's the deadlifts that do it. I don't use a Smith m/c for deads or SLDLs as I don't like the feel, even though there must be very little front-to-back motion with a free bar.
I do SLDLs for my hammies and my lower back. I used to stand on a bench and lower until the bar touched my feet. However, as the weight got heavier it gave me more lower back pain and also hip joint pain which was horrible. This cycle I have found that standing on the floor, which allows for a wider stance, keeping my legs just shy of fully locked out and lowering until the plates touch the floor is plenty deep enough. My lower back has been better and my hip joints have been fine.
So, it doesn't seem like you are doing anything wrong. It may just be too much volume for your lower back. I guess you could try alternating SLDLs with some weighted hyper-extensions and see how that works out. Or just do your SLDLs every other w/o and give your lower back a bit less to do. You will still be squatting after all.
Cheers,
Lol