You can get Blaze Powder by putting coal in a ProjectE Collector to let it go throught the upgrade process (1 item during the process is blaze powder). Also, there seems to be a weird recipe for Nether Quartz, it wants you to macerate Stone Stairs of Damage Value 7 (which i got no idea of how to get).
I would propose to change atleast 1 of the 2 Marble Blocks on the Portal to the Nether to Nether Quartz Blocks.
Also, it seems that once you got the SagMill you can Mill your Bones into BoneMeal which you get 6 bonemeal for 1 Bone (6 Bonemeal EMC > 1 Bone EMC). I don't know if this is intentional or not (especially because the DarkRoom Bonemeal Method from MC1.2.5 does not work anymore
)
PS: Also had to tinker around the MFE Detection Issue by Modifying the pyramid.