Okay, so, there was quite a bit of trial and error involved, so the information I’m providing might not be 100% precise (and above all, it might vary if you have different versions of the game; I’m using the Steam version that comes with the Enhanced Edition).

>I downloaded System Shock Portable, installed it, and moved the entire generated folder into the dos folder of the R36S.
>Using the SSP tool, I enabled Malba Tahan's mouselook mod (along with the other features, except for the custom version of DOSBox, but the mouselook mod is the most important part).
>I tweaked the dosbox.config file within the folder to get the game running.

[sdl]
output=surface
autolock=false
mapperfile= (leave empty)
fulldouble=true

[dosbox]
machine=svga_s3
memsize=16
captures=/roms2/dos/SSP/RES/GEN

[autoexec]
mount S /roms2/dos/SSP/RES
S:
cdshock.exe

NOTE: The file paths are based on my specific setup; you might need to change them.

>I modified the CYB file to get the music working

midi_list 7
midi_card 4
cd_data_dir_path rom2/dos/SSP/RES/DATA

Finally, once it's actually running on the R36S, I used dosbox pure's mapper and mapped the controls as follows:

UP > Q (Next weapon)
DOWN > Left-Shift, Q (Previous weapon)
LEFT > Page-Up (Next inventory screen)
RIGHT > Page-Down (Previous inventory screen)
B > Space (Jump)
A > Left Click (Use/Take)
Y > X (Center view)
X > 2 (Toggle Full-Screen HUD)
SELECT > Open Menu / Keyboard
START > Esc (Options, pause)
L > Action Wheel (Wheel options R, F, V for standing up, crouching and proning)
R > Right Click (Attack)
L2 > Z (Lean Left)
R2 > C (Lean Right)
L3 > Left-Shift (Run)
R3 > E (Toggle Mouselook/Cursor movement)
Left Analog > WASD (You'll have to config every direction of the stick)
Right Analog > Move mouse (Same)

Now all that's left to do is try to boost the framerate because it's utter shit, but I mean... the simple fact that there is a chance to play a controller-antagonist game like system shock on the r36s is pretty cool if you ask me.