I'm curious which version to be using at this point, since Dark's got deprecated and the original version was updated. I'm assuming you are intending to revert to the original, but the recipes are not entirely setup properly for it. Just from a few things I've noticed:
-Circuit Substrate Tier 1 used to require a lengthy process with the green algae, but now is switched to using Stone Brick -> Stone Tablet -> Fiberboard (??)
-Flasks require Iron Plates instead of Glass
-Clay Bricks are uncraftable, as they are looking for Angel's Clay instead of Py's Clay

There's probably more, but yeah

Also, are you planning on incorporating Py AL and Raw Ores at some point or is that never being added to this modpack?

Yeah, seems like the 1.0 release of the original PyCoalTBaA is having some problems. I'm going to report these issues to @kingarthur. May revert back to the temp version I was using before until things are more stable.

For the next major release of the pack I'm planning on integrating PyRawOres, but not PyAL since it looks like it makes tons of major changes revolving around plants and creatures that would break the progression and coherence with the rest of the non-Pyanodon mods. Still want this to be a tech focused pack.

I do want to mention that Py AL seems to be required to even have access to some buildings from the rest of the Py Suite. For example, without AL we were only able to craft Mk 1 Botanical Nursery, when it actually goes up to Mk 4. I understand from a workload perspective though, but I do feel that AL is probably being sort of shoe horned in by Pyanadon as an eventual requirement without a lot of recipe adjustments as an alternative.