I'm not sure what's preventing the buttons from fitting in your case, but if it's the tops of the LEDs, you may be in luck. I ground down the tips of my LEDs with a dremel to make my illuminated buttons fit better. Maybe that's all yours needs.

My experience is that LEDs are like cat's claws: You can grind away quite a bit of the tips without hurting the important bits at the base. looking at this picture you see that the actual diode bit is more than half way down from the top. That whole top section is just solid colored plastic, it's not hollow like a light bulb. I'd bet you could grind away 20-30 percent of the top of your typical LED and it would still work fine. (That's what I did on my button LEDs and they still work fine).