ok, posting what i've got. i won't be getting to the concordance of arcane space (or to the various other things that came in the boxed set, though i doubt most of those will have much) tonight, but i'll see if i can get to it later. i think 5 hours in one sitting is quite enough
Lorebook of the Void
Elminster (human male wizard, very high): 2, 13
** obviously not strictly an SJ NPC, just a borrowed name really. but he is there on the page.
Alliyah Makabuck (halfling , guessing female, almost definitely thief): 2
Large Luigi ("male" beholder): 12, beholder entry?
** (there doesn't seem to be a page number... it's page "70" of the PDF i bought from paizo many years back, but doesn't have a page number at the bottom. it's in the second page of the monster entry for beholders).
Khelben Blackstaff (human male wizard, very high): 13, 50
The Lord of Waterdeep (i have no idea): 13, 50
** (the entry on page 50 refers to the lord_S_ of waterdeep, which i believe is more correct. but i don't know FR lore that well... maybe there are multiple lords, and the most lordy lord of them all is *the* lord.
The Lord of Shadowdale (i have no idea for him either): 13
** the previous 3 are much like elminster; not spelljammer NPCs, just NPCs mentioned in spelljammer books.
Bloodjack of Realmspace (probably human, male, pirate captain): 38
** captain of the Lucky Victory below
the Grand Knight (h? paladin): 51, 52
** the grand knight is not strictly speaking an individual NPC, as the text indicates there is one per crystal sphere. they are the head of the company of the chalice within their sphere.
The Band of Seven Thieves: 53
The Starhunters: 53
The Lost: 53
** the previous three are adventuring companies, not individuals. no individual NPCs are detailed, but i thought i'd mention them.
Clevar (race, gender, and class unknown, or even if they're alive, though (s)he's the owner of a smuggling organization presumably which suggests thief levels): 53
Gaspar: (human male wizard I think): 53
** owner of Gaspar reclamantions. human and male are assumed. he is definitely a mage.
Grand Admiral (female elf, unspecified class): 55, 56
** the grand admiral is the leader of the elven imperial navy. there is also a council of admirals mentioned, which extends onto page 56. gender is mentioned briefly on page 56 when it mentions "her" staff.
Ub-Kalla (unknown gender, dracon god): the leader of the dracon gods. portfolio unspecified, but the spheres granted to dracon priests suggest protection and healing): dracon monster entry, 2nd page (probably page 72)
Dark God (uknown gender, spider-like god of the dracon, probably evil): same place as ub-kalla.
unnamed mage (unknown gender, race, or level): elmarin monster description (probably page 75)
Sirion the Flowing Flame (the god): page 87 (in the entry for Sirion the planet), 88
Reorx (the god): page 87 (in the entry for Reorx the planet)
Paladine: page 88
Takhisis: page 88
Chislev the Feathered Cleric (the god): page 89 (in the entry for Chislev the planet)
Selune (the goddess): page 93
Yggdrasil's Child (no gender, giant plant): page 95
** i have vague memories in realmspace that the plant that makes up Garden may or may not be sentient, blah blah blah... anyways, if you want to track the plant that makes up Garden, here it is
The Spelljammer (The Spelljammer): 3, 47-49,
the Rock of Bral (Asteroid city): 3, 7, 9 (very briefly as "the Rock"), 51, Scavver monster entry (probably page 85?), 87, 90-91, 94
** i'm not sure if it technically counts as a ship, but it shouldn't be too hard to keep track of just in case you want it.
Lucky Victory (pirate hammership): 38
The Company of the Singing Void's Man-O-War (Man-O-War) 40
** no particular information is given on the ship's actual name, or on the crew. the ship itself is a jet-black man-o-war.
Lionheart (Crown of Corellon): 55, 56
** the number of decomissioned armadas is left unspecified, but is noted as being one of the largest stations created from decommissioned armadas. lionheart explicitly does move to new hidden locations on a regular basis, however, so even if we're not going by nightdruid's fanon, i'd say it still qualifies as a ship.
possible unnamed dwarven citadel: 57