When i start the game it crashes while loading.
I am ussing Thaumcraft 4.2.3.5, Appliedenergistics 2 RV2 Beta 8 and ThaumicEnergistics 0.8.9.0B RV2.

Link: http://pastebin.com/L5JvCd2D

Did you try with the latest AE2? Quite a lot of stuff changed and it works fine for me.

I just tried updating AE2 to beta 13, but Minecraft still crashes while loading. I think that it is some kind of incapability with another mod because in FTB Infinitie it works just fine. I just cant figure out which mod it is.

try http://minecraft.curseforge.com/mc-mods/228513-loading-profiler. It is used to display the loading time of the installed mods. Maybe it will show at which point minecraft dies.

The issue from the crash log is that the second item for the Vis Relay Interface recipe is null
"Invalid shapeless ore recipe: 1xitem.ItemShard@6, null, 1xthaumicenergistics.item.aeparts@6"
The items is the ME P2P Tunnel. Which means it has been somehow been disabled, or something else is going on.
From your update it seems this problem is no longer present after you updated.