Issue with Pathfinder and Gradients

I'm trying to acheive an audio visualizer.. or sound bar that I will use in after effects later. I've created two shapes.  The first being the grid where I composed a graph, expanded it and then united it to make one solid shape.  Then I created a square, gave it a gradient from green to yellow to red, just like a sound bar. Everything looks fine but I want the black bars to be gone, I want to essentially create an inverse clipping mask with the black bars. But once I use the "minus front" in pathfinder, each  box takes on the gradient individually... Rather than keeping the original scheme... I will post pictures to explain.

I have tried saving the gradient image. But then when you go to use the pathfinder tool it will not work unless you trace, and expand the selection but that just creates a whole other mess... I feel like there should be some way to lock the gradient to the original form but I dont know how to do it?