I just installed the latest optifine to resolve the issue and it no longer says missing texture, however there is still a problem. The blocks that had missing textures are now using random textures from pam's harvestcraft. Also, I tried running minecraft after removing optifine and I get a black screen. Is optifine somehow holding my mods together so they all work? My only guess is that there may be conflicting textures and optifine may be doing it's best to keep minecraft running by using the same texture for multiple blocks.
(edit) I found out the textures get messed up when I have buildcraft installed.