I have installed Exnem's EyeCandy as well as HentaiGentleman's EyeCandy, together they work fine. However, when I put on upper body clothing, the upper body texture is replaced. I was able to tell this because with no upper body clothing/armor, the arms were not muscular. When I put on upper body armor/clothing, they became muscular and the torso changed slightly. What would be causing this? Is there any way to fix it?

The cause is that clothing and armor do not go over the upper body, they actually replace the upper body. The fix is to make that piece of clothing or armor with the arms you want.