What I've found out about the NEI crashes.. I did not find any differences between clicking or using 'u'/'r', so I don't think there's anything to do with that.
The crash log shows:
codechicken.nei.PositionedStack.setPermutationToRender(PositionedStack.java:95)
at yuuto.enhancedinventories.compat.nei.RecipeStoneCraftingHandler$CachedStoneCraftingRecipe.getCycledIngredients(RecipeStoneCraftingHandler.java:114)
- When Enhanced Inventories tries to put together the "Inventory Crafting" page from the Wool or Wood blocks, it crashes. This doesn't happen with cobblestone (the other ingredient in the Improved Stone Chest), so I think there's a problem with the way it's putting the list of all the woods/wools together for this screen. Easily replicated by looking at uses for any color of wool or any type of wood planks, and moving to "right" of the assembly tables page. The problem does not happen when looking at that recipe directly, just when it is generated from the wood or wool component. The only way I've found to fix it is to remove the mod.
Alternatively, don't look at the uses for wool or wood planks.
The crash log shows:
appeng.integration.modules.NEIHelpers.NEIInscriberRecipeHandler.loadCraftingRecipes(NEIInscriberRecipeHandler.java:98)
at codechicken.nei.recipe.TemplateRecipeHandler.loadCraftingRecipes(TemplateRecipeHandler.java:327)
This has been explained previously, but for posterity- if you load a world, everything is fine, but when you exit back to the Minecraft Main Menu and load any world again, you will hit the AE2 NEI crash when you look at a recipe you had previously looked at. This seems to be fixed by setting S:NotEnoughItems=OFF in the modIntegration section of the AppliedEnergistics2.cfg (not sure what impact this has - maybe disables shift-click into AE2 crafting interfaces?) Alternatively, reload the client between world loads.
If anyone has other reliable ways to crash via NEI, let us know!