The Full Map

Here's a preview of the full map. No, it's not even close to complete, as Maridia and Brinstar Green need to be added.

You will note that Brinstar Red (in the bottom) is way below the rest. That's because I there's not much space between Kraid's Lair and Ridley's Lair.

I find backtracking across Brinstar to be tedious, especially with the plethora of vertical shafts. Brinstar Red connects two fairly disparate sections of Brinstar, allowing an alternate route back once you've collected Bombs and the Ice Beam. Going further into Brinstar Red will require the Wave Beam and Screw Attack, and allow access to Maridia (which shortcuts to Ridley's Lair) and Brinstar Green (which shortcuts to Kraid's lair).

The Space Jump will be found in Brinstar Red, as will the Spazer Beam and Gravity Suit.
The Helix Beam will be found in Brinstar Green.
The Shock Beam and Burn Beam will be found in Maridia.

Obviously this is still a work in progress. I'll append more sections to this map as I go.