Okay, after looking into the problem, I realized that I uploaded the wrong .rul file. It was a junk file from a stray folder. I cleaned it up and everything should be working now. I updated the mod to 0.3. Use that version instead.
hellrazor mentioned that he didn't like my research system of having the ammunition types split up between Alloy and Elerium because it didn't give you all the items at once. I did that to give you improved weapons until you can get enough UFO parts to compliment the AP Alloy Weapons. idk about you guys but I use auto-cannons from start to finish in the game and the Alloy Assault Cannon is specifically built to reflect that.
