Squats are so important... I would avoid removing them from your routine... Perhaps look in great detail at the way you are performing them. If they are starting to irritate your lower back, you are most likely doing them incorrect.
Lower back pain can also come from dehydration... Are you drinking lots of water?
Are you stretching after your workouts? Are you warming-up properly? Stretch your lower back using an easy stretch for 30 seconds... Then, move into a deeper "developmental" stretch for 10-20 additional seconds.
Finally, it would be well worth the $50 it would cost to get a GOOD personal trainer to spend an hour with you perfecting your squat technique, lower back work, core muscle work, and legs. This will pay-off tenfold if the trainer helps alleviate your back pains.
I am currently training to become an NSPA CPT and know that a lot of the training we take involves working with clients that have lower back pain and trouble. I don't know about other organizations, but I imagine a personal trainer worth his salt will be able to help you leap past this issue and give you some strong advice for your legs and core to boot.
Just a thought,
Rip