Was just moving off from the crystal industry, when I noticed that none of the research for the crystal blueprints and schematics requires skills like the others do. ie. the sawmill blueprints requires architect, and just about all the schematics require student.
Also, you still have two identical '-- Research Crystal Forging Process(1t +)' in the Library reactions menu, one of which leads to the Crystal forging schematic, and the other leads to the Crystal smithing schematic.
After that I believe the crystal industry should be good, I'll be moving on to the weather factory in depth now.
*EDIT*
Just found one of those awesome bugs which looks a lot worse that it is.
[ITEM_TOOL:ITEM_TOOL_SCHEMATIC_LIGHT_CLOUDS]
[NAME:light cloud schematics:light cloud schematics]
[VALUE:100]
[TILE:136]
[SIZE:100]
[MATERIAL_SIZE:1]
[UNIMPROVABLE]
[ITEM_TOOL:ITEM_TOOL_SCHEMATIC_HEAVY_CLOUDS]
[NAME:light cloud schematics:light cloud schematics]
[VALUE:100]
[TILE:136]
[SIZE:100]
[MATERIAL_SIZE:1]
[UNIMPROVABLE]
They both have the same name in the game, so you'll have 2 light cloud schematics, but one of them is used for light clouds, and the other for heavy ones.
This one is hotfixable.
*Nother EDIT*
Another one, this one was a bit tougher to track down.
You forgot to include MAKE_CLOUD_CLOTH and MAKE_GOLDEN_SILK in the entities permitted reaction list for the magic loom.