I have no medical degrees, but have had experience with sports training injuries of others over the years. Also a personal experience with lower back (#3-4 disc) surgery while in college and recovery rehab'ing.
The lower back and the ab wall act together. Hence one will affect the other in functioning. Important that each is balance to strength and development.
Galain didn't mention his full training agenda, which may have an influence on his lower back problem also. Galain had mention the SLDL. I might suggest replacing that movement for a bit and adjust to Romanian Dl's. Check out youtube or other sources to do it correctly.
I will place my toes on a 2x4 for an extra stretch and general warmup for the chain of back muscles, hams & back. Using higher reps, lighter weight on the SLDL, GoodMornings or whatever exercise I choose. Sometime I'll clasp my hands behind my back and use no weight, feeling for a total stretch. Keeping the back straight, never rounded.
The Ab wheel is a very functional device for total Ab development (upper/lower and obliques). But some complain of the pressure on the lower back when using the device. Going to have to be your own judge when using it. We all respond differently to any exercise.
The ab's are a short range contraction muscle. Most short range contraction muscles are very powerful. Important the the lower back is not overcome by a much stronger ab wall. The doctor offered good advise, appears that you may have an imbalance.
Might suggest Ab crunches, lying on the floor with the legs drawn up (no weight). Try to feel not only the upper abs, but try contracting the lower abs also at the same time. This is when the mind come into play, a important element most BB'er have long forgotten. That would be total contraction the the complete ab wall, upper and lower. Hold that total contraction for three seconds, counted as one rep. Don't just want to rep out, but make every rep count. Taking a break from handing leg raise may be it's own reward for you.
Good Luck.