Agglomerator was developed for the sole purpose of being the perfect ID fixer and mod loader! This kind of utility is ideal for any modpack creator or hardcore mod fan! The only bug that has occurred when testing this was w/ the Advanced Solars IC2 addon alongside Engineer's Toolbox; its IDs get gridlocked somehow and have to be changed manually. Head over to the GitHub for the download, to view the source, or even help improve it! Enjoy!
You can simply pop it into your mods folder, load your game, and then remove it; it's effects will still remain! All of the IDs it fixes or changes can be found in the "agglomerator.txt" file that will be written to the overhead directory of the config folder.