New Texture System Z-Fighting and Glitches

The new texture system (each block and item have them and its states in their own separate image file) introduced in 13w02a brought a LOT of Z-Fighting into the game, also, it broke many textures, due to some missing files giving yourself some items crashes the game, for example, Nether Portal (ID 90) or End Portal (ID 119) have a pure white texture, redstone has weird breaking particles and if you give yourself a Monster Spawner (ID 52), the game just crashes.