You need to get into Aura Cascade before anything, hence the Arcane Black Ingots in the recipe, but that stuff is unchanged so I didn't spotlight it. After this, get Pure Dasy, make Livingwood and Livingrock, and then get some mana going! But what about the Runic Altar? Well...
You do need Arcane Black Ingots for this, as well as two Mana Pearls and one Mana Diamond. Simple enough. The runes I did change the recipe of to be more structured though.
The first tiered runes (as seen above) require various Arcane Ingots along with three decorative things from Botania: A Pasture Seed type, a piece of special Quartz and two types of Metamorphic Stone. Second tier runes require two 1st tier runes and two types of Arcane Gem, and the third tier requires a first-tier rune, a second-tier rune and an Arcane Prism. But for the tier two and above, you'll need some Vortex Infusion! How do you get that?
...With a Rune of Mana, of course! The Controller is made with Mana Diamonds, Gold, Arcane Red Ingots and said Rune, along with the Pedestals being made by infusing the regular Aura Nodes with a bit of Mana. And also, the Arcane gems are a bit different.
They require Mana Diamonds instead of regular ones. Once you craft these, you can make a Prism to use for your Terrestrial Agglomeration Plate. But wait! How do you make that?
To get into magical crops you will need to build a elven gateway and create a dragon stone. This will allow you to make the Infusion stone and get into the final section of the good magic.