Please comment if you have additional I.J.-Boston locations.
1. Antitoi Entertainment, Inman Sq. (p.480, not real)
2. Ryle's Jazz Club (p.479)
3. "Cambridge Theatre Company that seemed to do only German plays" [a.k.a. the A.R.T.] (p.18-19)
4. Live Poultry Fresh Killed (p.479)
5. Blanchard's Liquors in Allston (p.546)
6. Marlborough st. art gallery (p.23)
7. Brighton Projects (p.38, 130, 131) [Charlesview apartments at Harvard+Western Ave in Brighton?]
8. Winchester High School (p.39, [Mildred Bonk + Bruce Green's h.s.])
9. Mount Auburn Club (West Watertown, p.34) [wow... it really exists]
10. Newton-Wellesley Hospital (p.69 [Gompert gets electrochock therapy there, also, incidentally, I was born there])
11. Steve's Donuts in Enfield Square (p.129 [I thought it was Steve's Bakery in Somerville but then they go on to say hang out in Enfield Square...in Enfield or Allston, p.131])
12. Bow+Arrow Pub, Harvard Sq (p.129) [c.f. "do you like apples"]
13. CVS in Central Square (p.129)
14. Cheap-O records (central square) (p.129)
15. Hung Toys, Chinatown (fictional, but definitely sex shops in C-town, p.132)
16. "hot air blowergrate we use at nite at the library behind the Copley Squar...behind the brickworks behind the bush by the hot blowergrate" (p.133)
17. Dwayne R. Glynn, 176N Faneuil Blvd, Stoneham, MA (no Faneuil blvd in Stoneham, p.139)
18. Enfield: best geography given p.240-242, "arm-shape extending north from Comm Ave and separating Brighton into Upper and Lower, elbow nudging East Newton's ribs and its fist sunk into Allston" [then a long list of businesses that I'm not going to google right now] "...ETA hilltop overlooking on one side, east, historic Comm Ave's acclivated migration out of the squalor of Lower Brighton --...the huge and brooding Brighton Project high-rises with three-story-high orange ID-numerals on the sides [c.f. #7]...quarter-hourly trundle and ding of the Green Line train's labor up the Ave.'s long rise to Boston College...from both the north and northeast tree-lines ETA looks down its hill's steepest, best-planted decline into the complexly decaying grounds of Enfield Marine."
19. The Globe's map of Joelle's foot journey is good, but for the record: "wet walk here from Red Line's Downtown stop, walking the whole way from East Charles St...approaches boston common...a store 24...common's south edge is Boylston St...boylston st east means she pases statue of boston's colonel shaw and th eMA 54th...raised sword illicitly draped in a large Quebecois fleur-de-lis flag [by the Antitoi, ~487]...f.a.o. schwartz [where the weird tape dispenser statue is located]...along boylston...to Upper Brighton and the cooperative Back Bay-edge brownstone" (p. 224-227)
20. "Bogart's in Porter Sq." (non-existent, p.20)
21. MIT student union (p.186-187)
My dad has two pretty good suggestions: first, he pointed out that the Longwood Cricket Club (google: "The Longwood Cricket Club may not be the oldest tennis club in the nation, but it continues to lure the best professional competition in the state...") is right in the area that we identified as potential ETA territory.
Second, he made the assertion that "___ Spur" always referred to a neighborhood around a spur in the railroad, not the highway, though made no suggestions about potential railroad spurs in Allston. He did say that the area east of Harvard Ave on Comm Ave used to be a pretty bad neighborhood (though I think that's more Brighton...). You can see the railroad tracks on google maps, if that helps. When Erdedy's buying pot on p.18, he buys it from a woman who "said she knew a guy just over the river in Allston who sold high-resin dope in moderate bulk," and that guy is most definitely the dude with the hairlip.