This page-by-page annotation is organized by sections, as delineated by the seven squares (sprockets) which separate each section. The page numbers for this page-by-page annotation are for the original Viking edition (760 pages). Editions by other publishers vary in pagination the newer Penguin editions are 776 pages; the Bantam edition is 886 pages.
Contributors: Please use a 760-page edition (either the original Viking edition with the orange cover or the Penguin USA edition with the blue cover and rocket diagram there are plenty on Ebay for around $10) or search the Google edition for the correct page number. Readers: To calculate the Bantam edition use this formula: Bantam page # x 1.165. Before p.50 it's about a page earlier; as you get later in the book, add a page.
Finally, profound thanks to Prof. Don Larsson for providing the foundation for this page-by-page annotation.
38.4-5 you’ve been able to shoot back now and then at the odd flying buzz bomb
The pulse-jet-powered V-1 "buzz-bomb," flying at 400 mph, could sometimes be intercepted by both anti-aircraft guns and propeller-driven fighters. The V-2 rocket, at 3500 mph outside the atmosphere and half that speed on impact, could not.
38.6 "dear old Nutria-"... "Beaver."
The nutria (Myocastor coypus), also known as the river rat, is a large, herbivorous, semiaquatic rodent and the only member of the family Myocastoridae. Originally native to subtropical and temperate South America, it has since been introduced to North America, Europe, Asia, and Africa, primarily by fur ranchers. Although it is still valued for its fur in some regions, its destructive feeding and burrowing behaviors make this invasive species a pest throughout most of its range. 
38.19 watching that awful Going My Way
Going My Way is a 1944 film directed by Leo McCarey. It is a light-hearted musical comedy-drama about a new young priest (Bing Crosby) taking over a parish from an established old veteran (Barry Fitzgerald). Crosby sings five songs in the film. It was followed the next year by a sequel, The Bells of St. Mary's. This picture was the highest-grossing picture of 1944. Its success helped to make movie exhibitors choose Crosby as the biggest box-office draw of the year, a record he would hold for the remainder of the 1940s. 
38.21 each saccade of her... eyes
Saccades are quick, simultaneous movements of both eyes in the same direction. 
38.36 It was what Hollywood likes to call a "cute meet"
On p.561, Pynchon has Slothrop singing "LOOK-IN’ FAWR A NEEDLE IN A HAAAAY-STACK!" which is a song from the Fred Astaire/Ginger Rogers film The Gay Divorce (1934). In that number, Astaire sings about finding the woman of his dreams whose name he never learned after they had had a "cute meet."
Pynchon uses 'cute meet' again in Inherent Vice p. 37
38.37 Tunbridge Wells
Royal Tunbridge Wells (usually shortened to Tunbridge Wells) is a town in west Kent, England, about 40 miles (64 km) south-east of central London by road, 34.5 miles (55.5 km) by rail. The town is close to the border of the county of East Sussex... Due to its position in South East England, during the First World War Tunbridge Wells was made a headquarters for the army, and its hospitals were used to treat soldiers who had been sent home with a "blighty wound"; the town also received 150 Belgian refugees. The Second World War affected Tunbridge Wells in a different way – it became so swollen with refugees from London that accommodation was severely strained. Over 3,800 buildings were damaged by bombing, but only 15 people lost their lives. 
38.39 ATS skirt
British ATS: British Auxiliary Territorial Service
Possible reference to Wallace Stevens' poem, "Variations on a Summer Day": Words add to the senses. The words for the dazzle / Of mica, the dithering of grass, / The Arachne integument of dead trees, / Are the eye grown larger, more intense.
The mica group of sheet silicate (phyllosilicate) minerals includes several closely related materials having highly perfect basal cleavage. All are monoclinic, with a tendency towards pseudohexagonal crystals, and are similar in chemical composition. The highly perfect cleavage, which is the most prominent characteristic of mica, is explained by the hexagonal sheet-like arrangement of its atoms. 
40.13 Psi Section
The Greek letter psi was first used in 1942 to signify "the unknown factor in extrasensory perception and psychokinesis experiences that is not explained by known physical or biological mechanisms." 
all the definitely 3-sigma lot
A statistician's shorthand for "very unusual people." It means three or more standard deviations from a mean or typical value, the extreme outlying values (both high and low) of the familiar "bell curve." Only about 2% of a random population sample would be expected to score "3-sigma" on various psychological scales. 
40.18 the chi-square calculations, in between the flips of the Zener cards...
The chi-square test is one of the most common statistical procedures, used to determine if a data set differs from what would be expected if nothing abnormal were affecting it (i.e., to separate "signal" --if any -- from random "noise"). Zener cards are cards used to conduct experiments for extra-sensory perception (ESP), most often clairvoyance. Perceptual psychologist Karl Zener designed the cards in the early 1930s for experiments conducted with his colleague, parapsychologist J. B. Rhine. 
40.21 fire control The use of statistical models to direct anti-aircraft fire. For most of WWII, gun crews used timed fuses to detonate shells within a certain range of altitude, hoping to fill the "box" through which bombers were flying with shell fragments and shock waves. Later, proximity fuses with miniaturized radar electronics would detonate when the shell was closest to an aircraft, making AA fire much more effective.
40.34 Battle of Britain
The Battle of Britain was the most intense period of air combat between the German air force (Luftwaffe) and the UK's Royal Air Force (RAF) during the summer and autumn of 1940. The objective of the campaign was to gain air superiority over RAF Fighter Command, while bombing British targets ("the Blitz") to force surrender or prepare for an invasion. The name derives from a famous speech delivered by Prime Minister Winston Churchill in the House of Commons: "...the Battle of France is over. I expect that the Battle of Britain is about to begin."
The Battle of Britain was the first major campaign to be fought entirely by air forces. From July 1940 coastal shipping convoys and shipping centres, such as Portsmouth, were the German bombers' main targets; one month later the Luftwaffe shifted its attacks to RAF airfields and infrastructure. As the battle progressed it also targeted aircraft factories and ground infrastructure. Eventually it shifted to targets of political significance and urban areas, with less frequent raids extending into May 1941. The failure of Germany to achieve its objectives is considered its first major defeat and one of the crucial turning points in the war. 
Same make of car as in the beginning of V. A high-quality luxury vehicle.
41.28-29 barrage balloons south of London
Barrage balloons were blimps tethered with steel cables, used to make it more difficult for attacking bombers to line up their approach and keep formation.