Reddit mentions of Exo Terra Sepia Bones for Turtles

The rounded edges and the lumps on her carapace are definitely abnormal for a RES. A healthy adult's shell should be smooth and slightly domed like this. Unfortunately most shell malformations are irreversible once they form, but improving her habitat/diet can help keep the problem from getting worse and give her a more comfortable life. I'll address the three concerns you outlined, as they could all be contributing to this issue.

A) A good rule of thumb for appropriate tank size is 10 gallons per shell inch (measured in a straight line from the front to the back of the carapace) of turtle. At the very least, she needs a tank wide enough for her to turn around comfortably and long enough to swim back and forth a bit. A 30yo slider should be much larger than 4", so 40gal likely wasn't enough space for her. If she was constantly pressed against the sides of the tank because it was too small, it could cause the edges of the shell to curl up like that. Depending on the actual size of your turtle, you are probably going to need a much larger tank, along with a good filter to keep it clean.

B) Poor diet can cause shell malformations as well, but I don't think they usually look like this. Having too much protein can cause pyramiding (when each scute becomes tall and pointed, rather than smooth), but your turtle's carapace has more of a lumpy-pancake shape. My (inexpert) guess would be that she has a calcium or vitamin D deficiency that prevented normal shell growth. You can improve her diet by providing her mostly with lettuce and other leafy greens (which have a good amount of calcium in them) and just supplementing with pellets or other treats. You can also buy sepia bones as a direct calcium supplement. The possible vitamin D deficiency can be addressed with an improvement in lighting.

C) Your turtle will need two kinds of lighting (which may mean buying two sets of lamps and bulbs): a heat lamp and a UVB source. Having a heated basking area is important for them to digest their food properly and maintain other bodily functions, and UVB is essential for vitamin D production and calcium absorption. Any heat bulb that warms the basking area to about 90 degrees F (or 10 degrees warmer than the water) should be okay. For UVB, my vet recommended using a bulb with a "spiral" shape instead of a "U" shape because he thinks it helps transmit more light downward toward the basking area instead of out to the sides.

Aside from those three things, I would strongly recommend visiting an exotic pet vet (or herpetologist, if there's one close enough to you). Since your turtle is new to you and her previous living conditions weren't exactly ideal, it's possible that she's suffering from other conditions as well. A vet should also be able to give you more specific advice for habitat and diet improvement. Good luck with your new turtle!