Alright, I finished a temporary fix. I also updated the main map with a few tiny things that needed fixing, namely the block of sandstone in the desert island and the two stacks of hives in the white enderchest. If you already have a world, then please dispose of those hives, not use them. They are not intentional and were only there because they are not available in NEI, so I had to /give them to myself in order to use them. The sandstone isn't as big of an issue, but still needed fixing. You do not need to start over if you have already started, these changes are extremely minor.
The transmutation recipes are very temporary, so I decided to give them their own book instead of putting the recipes in the main book just to delete them later. To see the recipes, you will need to craft the recipe book for the transmutations, called the Alchemical Tome with one thaumonomicon (which is required because if you can make one then you already have the capability to research them and see the recipes if they existed) and one gold ingot (my system doesn't like 1-ingredient recipes for some reason and I don't feel like fixing it to accept them.). The recipes will be in the system until they are no longer needed, at which point they will be disabled, but not removed, in case I need it again.
Also, I'm going to make a second version of the map with absolutely no hand-holding. You only get the materials and recipes that you need, no more and no less.