Basically I was using the most inefficient algorithm ever. I was lamenting this suffering to a friend of mine and he gave me an algorithm that did it in less than a minute for each data set. All I was doing was binning the data, and Excel doesn't have a built in function for that. The postdoc in my lab told me to use the SUMIF() function, which has the issue of needing to check every single data point on every iteration. These spectra are of massive gold clusters (we're characterizing our primary ions right now) with over 600,000 data points, so you can see why that might take a while. I dropped the last 350,000 iterations (I actually misspoke earlier) on that data set because our collection window had been a bit too large (it was around 1.2 million data points) and was picking up a second projectile, and we weren't really that interested in the noise past the peak* anyways.
*blob/distribution
But yeah, my friend's algorithm trivialized that and saved me around four hours.