Lots of info there, some thoughts:
edit:meh, tags giving me all sorts of issues so back to ascii bullet points

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Civilized space:
-The artificial city sounds like a great place to set up as a mini-dyson sphere or ringworld. You can also go with labyrinthine maze that defies casual description, but there is a great deal to be said for simplicity of visualization.
Pseudonatural world:
-Perhaps make it so that the star which the gas giant revolves is corrupted/different from the other stars in the crystal sphere.
-Alternatively, have the gas giant actually be a dwarf star which provides sustenance to the dark world (functionally the only difference between this and your description would be that the pseudonatural world would be visible as a star in the night sky of other worlds). Your description makes me think that the pseudonatural world is just freefloating without a starsystem, dunno if that's what you intend.
Frontier Space:
There are seemingly two ways of envisioning frontier space - that of star systems out at the edges of the crystal sphere which are at such distances as to make travel dangerous/intolerably expensive, or frontiers around the periphery of each inhabited system.
The former would fit settings where you want the frontier races to be more mysterious/unknown. Either as implacable, alien enemies or nearly incomprehensible, but powerful, allies. The latter is better suited to more mundane villian of the week scenarios.
I'd recommend the former, with the star systems being strange in some way for each frontier race you wish to add. For example, the formian star system could appear to be a dim red dwarf out at the periphery of space, but as you approach you see that it is actually a series of linked habitats that dissipate heat the formians create externally - shining a dull red in the process. A bit more mundanely, a frontier star system could have weird laws of physics as compared to the rest of the crystal sphere, where gravity is weaker than normal, space is actually breathable, stars rotate around planets, that sort of thing.
Cosmology and magic:
It seems you set up the system so that there are four planes - prime, astral, ethereal, and far realm. Spelljamming would be a setting specific magic for this sort of system, but also tapping the various planes for power (spelljamming becomes a subset of that). If astral can be tapped for increased travel speed in spelljamming, you might see more mundane uses such as carriage enchantments that make them swifter, teleportation magic that is actually astral manipulation, etc. You'd have some spells which have different interactions with the gameworld than the phb would suggest (i.e. teleportation) and possibly require some reexamining/rewriting of rules as well as more specific and limited magic (carriage speed boost).