Based on Jaguar King's Tutorial. This is what I wrote during the 12 hour challenge to keep track of the details. A better guide would use screenshots, etc. But this may help you in getting started.
Basics
Line of Sight is a straight pixel.
To increase rank, rescue POWs or interrogate officers.
We'll be saving POWs, not interrogating.
You'll need to get 4 rank ups for the run.
Press A once to skip text box
Elevators are checkpoints for continues
If you are at max rations and a ration drops, eat a ration, then pick it up.
Single Exclamation Mark Alerts mean you are fine to go into the next screen. Double Exclamation Mark Alerts stick between screens.
Alert guards don't drop stuff
Button controls are flipped on Sidescrolling sections
JUNGLE
Second Copter screen, go to left edge of dark
Green path, then move up once the Copter leaves
First spotlights, go left for rations
After ration detour, hug tower on right
Go up for POW #1
hug right wall when exiting from 1st POW
Continue right
Watchtower car, three spotlights
Enter from bottom to the main gate
Answer Codec for the only time in the speedrun
FORT 1
First 2 guards in Fort 1, right guard viewpoint is random
Get Card 1 in the left room
Revisit the Jungle to get the silencer by going north
After silencer, go up for POW #2, up at Watchtower
Return to Fort 1
Go down the right path
Upper path for POW #3
Next guard is a single ! alert, so run up and right to exit the alert
Card 2 is in the far right door
Go up on the left side for POW#4
Run upleft for the elevator
Fort 1 B1
These guards turn randomly
Hug the shadow wall
Kill enemies if you get an alert
Take the left path
Enter far left door for explosives, you need 15 (3 trips)
Punch guard outside of long hallway for ration potential drop
At camera junction, go down
Card 2 Door, get 3 each of grenades and ammo
When going right for cameras go up on then the wall, then go right once the right camera goes down
Fort 1 B2
Can punch guards for rations/ammo
Try to max out for 4 rations
SIDESCROLLER 1
Equip pistol and shoot the first guy
don't bother with the knife
Use i-frames of losing hp from water to walk through last mine
FOOTBALL TACKLERS
Equip explosives
the moment you hit return, plant bomb
Go right, when they hit you, go left
Plant bombs on the opposite corner of the alcove, go to corner and turn
When they start running, go to opposite side
1 guy left,finish him with the pistol
re-equip pistol at end of fight
Can punch guys for resources
The blocks before boat, position perfectly
pay attention to block above
punch, then open the door immediately (downright movement)
Alternatively, knife the block until it breaks
When exiting to outside, go up immediately
go right, shoot dudes, enter the ship
SHIP
Shoot or punch the dude
Enter the elevator
Ship B1
Go right path, but enter next room at bottom
can punch or shoot the guy
hug right wall, go up top
Card#1 to enter fight room
Equip grenades/ration before entering
KARNOVs
Grenade explosives have huge hitbox
Kill middle, then left, then third
Go left then up, you can throw 2 nades
Do a rectangular movement for each pair of throws
Finish with explosives on sandbags
Get card #3
Open left door for mine detector as you go back (optional)
Retrace your steps to elevator
Ship B2
Run up to the guy and punch him (Single ! Mark)
Can use a ration before entering Metal Gear room
Sensors can be random
up, right, down, right in movement
enter the door to blow up ammo
Plant explosives as close as possible to the door
Return to elevator
Equip card 2 entering elevator
Top floor
Go right
Enter door
Go right
Go up
FORT 2
Hug left bricks, go up
Hug left wall, go up
Go left after corner, hug wall, go up
go up, along the wall
Equip Card 1
RC missiles and rations
Optimal just 4 for each
Playing safe, max rations to 9
You can move a bit down to avoid RC missiles
Hug the sandbags
Enter up room for POW#5
Go right, up, get max oxygen tanks - 5
Optimal is 4
stand by left wall and destroy sandbags
RC the dude
SIDESCROLLER #2
Equip pistol
Mine movement is random
Dip down under the camera
Jump to next screen
Watch out for sensors
Shoot the sensor, space out shots due to i-frames, 4 bullets needed
TRAIN
Shoot guard blocking you from train l
You can farm the first two guards, Single ! area
First Needle Room
Go right, up
Wait on first box on right
Going optimally, be patient
If you have extra rations, blast thru
Careful on bridges with your movement, or you can die
Shoot that guy on the train car
Punch or shoot these 2 guards
Punch or shoot guard at door
Second Needle Room
Go up the right side, stand by the box
Enter first room for POW#6
Second room, TRAP, go down immediately to pick up card 4
Backtracking in Second Needle Room
Hug box, go down, left, down
Enter the room in next car
Equip RC missile, card 4
"John Turner" Spy
Hold right when entering room, activate TRAP
Hold left when trap is activated
Need at least 4 hp to touch spy
Time your shots, due to i-frames
Stand middle, shoot , shoot, shoot
Ration up after two hits if at max
If you run out of RC missiles, finish with explosives
FORT 3
Go up, exit car from bridge
Punch guy
Go to door, equip card 4
Need 2 explosives, but pick up 3
Equip armor
Go left
Push block by holding the direction
Plant an explosive between two black windows
Equip the knife!
Card 1 Door, POW#7
Enter next screen, stand on right edge, shank 'em
Blow up left wall and rush in
Blow up right wall equip armor, push bottom block
Card 2 Door, POW#8
card 3 Door on right
Platforms
Be careful on the platforms! It stinks to die here.
Time last platform correctly
Plant explosive on right wall
Plant explosive on left wall
Plant explosive on bags
Stab dudes while you wait
SIDESCROLLER #3
Stab the dude with a jump
Crawl into second screen, stab 'em
Continue crawling in next screen
Crawl into next screen
Random looking for 2nd guard
Jump and knife
Crawl into next screen
Crawl into next camera, walk, drop back to crawl for next screen