Here is a diagram showing how the alchemy reactions link together if it helps anyone use alchemy.
Dotted Ovals = alternative ways to make something.
If you want to recreate or tweak the diagram here is the data to create the graph using the free GraphViz program.
digraph G {
ratio=compress;
size=16;
// minable
Cinnabar [shape=box];
Cobaltite [shape=box];
Stibnite [shape=box];
Melanerite [shape=box];
Chalcanthite [shape=box];
Bauxite [shape=box];
Alunite [shape=box];
"Alum Slate" [shape=box];
"Rock Salt" [shape=box];
Talc [shape=box];
Olivine [shape=box];
Dolomite [shape=box];
"Frost Crystal" [shape=box];
Fireheart [shape=box];
"Storm Crystal" [shape=box];
"Ward Crystal" [shape=box];
"Flare Crystal" [shape=box];
Saltpeter [shape=box];
Truesilver [shape=box];
Levitite [shape=box];
// bars
"Crystal Glass" [shape=triangle];
Mithril [shape=triangle];
Levisium [shape=triangle];
Gold [shape=triangle];
Platinum [shape=triangle];
Tin [shape=triangle];
Silver [shape=triangle];
Copper [shape=triangle];
Iron [shape=triangle];
Glacium [shape=triangle];
Incendium [shape=triangle];
Tempestium [shape=triangle];
"Ward Iron" [shape=triangle];
Elementium [shape=triangle];
"Blazing Incendium" [shape=triangle];
"Bright Silver" [shape=triangle];
"Royal Bronze" [shape=triangle];
"Verdant Bronze" [shape=triangle];
"Green Copper" [shape=triangle];
Orihalcum [shape=triangle];
"Tempered Crystal" [shape=triangle];
"Night Crystal" [shape=triangle];
"Blood Crystal" [shape=triangle];
"Void Crystal" [shape=triangle];
// Plant
"Oil Nut" [shape=box, style=dotted];
"Tunnel Tube" [shape=box, style=dotted];
// Structal
Oil1 [width=.37, height=.25, fontsize=10, style=dotted];
Oil2 [width=.37, height=.25, fontsize=10, style=dotted];
Alum1 [width=.37, height=.25, fontsize=10, style=dotted];
Alum2 [width=.37, height=.25, fontsize=10, style=dotted];
Alum3 [width=.37, height=.25, fontsize=10, style=dotted];
"Emen Aren1" [width=.37, height=.25, fontsize=10, style=dotted];
"Emen Aren2" [width=.37, height=.25, fontsize=10, style=dotted];
"Ikal Nabid1" [width=.37, height=.25, fontsize=10, style=dotted];
"Ikal Nabid2" [width=.37, height=.25, fontsize=10, style=dotted];
"Ikal Nabid3" [width=.37, height=.25, fontsize=10, style=dotted];
Vitriol1 [width=.37, height=.25, fontsize=10, style=dotted];
Vitriol2 [width=.37, height=.25, fontsize=10, style=dotted];
Potash -> Saltpeter;
Fuel -> Quicksilver;
Cinnabar -> Quicksilver;
Oil -> "Midnight Elixir" [weight=5];
Cobaltite -> "Midnight Elixir";
Fuel -> Antimony;
Stibnite -> Antimony [weight=5];
Fuel -> "Green Vitriol";
Melanerite -> "Green Vitriol";
Fuel -> Vitriol1;
"Green Vitriol" -> Vitriol1;
Fuel -> Vitriol2;
Alum -> Vitriol2;
Vitriol1 -> Vitriol;
Vitriol2 -> Vitriol;
Chalcanthite -> "Blue Vitriol";
Potash -> Alum1;
"Alum Slate" -> Alum1;
Potash -> Alum2;
Bauxite -> Alum2;
Potash -> Alum3;
Alunite -> Alum3;
Alum1 -> Alum;
Alum2 -> Alum;
Alum3 -> Alum;
"Green Vitriol" -> "Emen Aren1" [weight=5];
Saltpeter -> "Emen Aren1";
"Blue Vitriol" -> "Emen Aren2" [weight=2];
Saltpeter -> "Emen Aren2";
Alum -> "Emen Aren2";
"Emen Aren1" -> "Emen Aren";
"Emen Aren2" -> "Emen Aren";
"Rock Salt" -> Salt;
Vitriol -> "Nabid Ubal";
Salt -> "Nabid Ubal";
"Nabid Ubal" -> "Relon Aren";
"Emen Aren" -> "Relon Aren";
Talc -> "Ikal Nabid1";
Olivine -> "Ikal Nabid2";
Dolomite -> "Ikal Nabid3";
"Ikal Nabid1" -> "Ikal Nabid";
"Ikal Nabid2" -> "Ikal Nabid";
"Ikal Nabid3" -> "Ikal Nabid";
"Relon Aren" -> "Frost Elixir" [weight=5];
"Frost Crystal "-> "Frost Elixir";
"Relon Aren" -> "Fire Elixir" [weight=5];
"Fireheart" -> "Fire Elixir";
"Relon Aren" -> "Storm Elixir" [weight=5];
"Storm Crystal" -> "Storm Elixir";
"Relon Aren" -> "Ward Elixir" [weight=5];
"Ward Crystal" -> "Ward Elixir";
"Relon Aren" -> "Pure Elixir" [weight=5];
"Frost Crystal" -> "Pure Elixir";
Fireheart -> "Pure Elixir"
"Storm Crystal" -> "Pure Elixir";
"Ward Crystal" -> "Pure Elixir";
"Relon Aren" -> "Blaze Elixir" [weight=5];
Fireheart -> "Blaze Elixir";
"Flare Crystal" -> "Blaze Elixir";
"Frost Elixir" -> Glacium;
Iron -> Glacium;
"Fire Elixir" -> Incendium;
Iron -> Incendium;
"Storm Elixir" -> Tempestium;
Iron -> Tempestium;
"Ward Elixir" -> "Ward Iron";
Iron -> "Ward Iron";
"Pure Elixir" -> Elementium;
Iron -> Elementium;
"Blaze Elixir" -> "Blazing Incendium";
Iron -> "Blazing Incendium";
"Oil Nut" -> Oil1;
"Tunnel Tube" -> Oil2;
Oil1 -> Oil;
Oil2 -> Oil;
Truesilver -> Mithril;
"Emen Aren" -> Mithril;
Levitite -> Levisium;
"Emen Aren" -> Levisium;
Mithril -> "Bright Silver";
Silver -> "Bright Silver" [weight=4];
Mithril -> "Royal Bronze";
Tin -> "Royal Bronze";
Copper -> "Royal Bronze" [weight=4];
Levisium -> "Verdant Bronze";
Tin -> "Verdant Bronze";
Copper -> "Verdant Bronze" [weight=4];
Levisium -> "Green Copper";
Copper -> "Green Copper" [weight=3];
Mithril -> Orihalcum;
Gold -> Orihalcum;
Platinum -> Orihalcum;
"Crystal Glass" -> "Tempered Crystal";
"Ikal Nabid" -> "Tempered Crystal";
"Crystal Glass" -> "Night Crystal";
"Midnight Elixir" -> "Night Crystal";
"Crystal Glass" -> "Blood Crystal";
"Ikal Nabid" -> "Blood Crystal";
"Quicksilver" -> "Blood Crystal";
"Crystal Glass" -> "Void Crystal";
"Ikal Nabid" -> "Void Crystal";
"Quicksilver" -> "Void Crystal";
"Midnight Elixir" -> "Void Crystal";
Antimony -> "Void Crystal";
};