I got distracted and kinda forgot about minecraft, that's why it was delayed by a few weeks. Really it's just a matter of going through all the dusts in NEI and working out the correct outputs and ratios, sometimes I just don't bother though and approximate. So far it's only happened for red alloy ingots and steel but there are issues with GT's perfect splitting system and Minechem's 16 based system as they clash horribly, for example there is one carbon atom per 200 iron atoms in GT steel, that can't really be represented or balanced so I just left it no carbon as that's trivial to get and it makes things much simpler. On another hand the only farmable source of magic for the various source of magical elements are thaumium and ender pearls, it's required for a bunch of random stuff from mithril to nether stars.
One advantage of this slog though, once it's done once it basically doesn't need to be done again. Unless they change the composition of various metals or add alloys most of the list should still be valid, with a bit of a script you could probably even mass do it for all of the different parts, the only trick would be figuring out the id's they use and making a list of all metals which can be used for the parts but that's relatively easy with NEI dumps.
Basically though it's just motivation and laziness that was the issue, I've started again though, have to decide between trying to join the server and starting an SSP world to really get my going though, that and I want to actually start playing again. Anyone who goes on the server capable of recommending it? My main requirement is that it won't shutdown in a month, that's been a serious issue as every server I've ever tried has done so, admittedly I haven't tried more than a couple as it put my off.