I´ve tinkered for hours getting finding a comfortable way to play the game on keyboard and mouse.

I found no guides to help me, so I´ll tell you how I´ve done it. It´s alright for me, but you can simply swap controls till you feel comfortable with it.

I use a software called keyboard splitter (https://github.com/djlastnight/KeyboardSplitterXbox/releases/download/2.2.0.0/Keyboard.Splitter.2.2.0.0.zip) which emulates an Xbox 360 controller.
You will have to set these yourself, but I will list you all the keybindings.

The keybinds take a little time to get used to and its a bit of a compromise, which favors better gameplay settings, but has some unconventional menu controls on the other hand.

After you set and activated your control scheme in keyboard splitter you´ll have to run it with the "Block keyboard" option enabled.
You can also quick toggle this mode with pressing CTRL five times.

I will list the controls and explain how to use it first and list the bindings afterwards.

I hope you can finally enjoy MGS3 as much as me.

W and S for Up and Down
Space for Enter
F for going Back

I have a mouse that has two extra buttons I can use with my thumb. You may have to find your own keybinding, if you don´t have spare mouse buttons. You can set mouse buttons, when hover your mouse over the little mouse symbol in the bottom right of the little input window, when setting up a certain key).

Mouse for looking around, no need to set anything. Your mouse works along the emulated controller. I had to set my mouse sensitivity to almost 10x my normal DPI.

WSAD for Movement
Spacebar for Crouch/Lay/Stand
IJKL for Quiet Movement (I found no better soultion for this)

Q for Item Menu
E for Weapon Menu
Tab for Radio
ESC for Menu (Backpack, Camo, etc)

Right Mouse Click for getting your gun into Aim Mode without firing
Left Mouse Click to Shoot
Extra Mouse Button for Ego Perspective (required for ADS)
SHIFT for ADS
F for Melee and CQC Combat. While holding an enemy in CQC hold right mouse click for Interrogation, R for Killing and F repeatedly for Choking
R for Actions (climb, open things, pull yourself up when hanging on a ledge)
V for the zoomed out view (I wouldn´t use it, though, but I think it could be useful in some scenarios)

Button Start - Escape
Button Back - Tab
Left Thumb - MouseRightButton
Right Thumb - V
Left Bumper (LB) - LeftShift
Right Bumper (RB) - MouseExtraButton
Button Guide - None
Button A - Space
Button B - F
Button X - MouseLeftButton
Button Y - R
Left Trigger (LT) - Q
Right Trigger (RT) - E
Axis X Min - A
Axis X Max - D
Axis Y Min - S
Axis Y Max -W
Axis Rx Min - None
Axis Rx Max - None
Axis Ry Min - None
Axis Ry Max - None
D-pad Up - I (Capital i)
D-pad Down - K
D-pad Left - J
D-pad Right - L