So I reinstalled this today and got the Deathwish mod to work (for the most part). However after setting things up to work with my system I can't seem to launch the game properly with a shortcut, It boots up and plays, but my mouse doesn't work, I assume it's not booting up bmouse.exe when it should be (it's in the cfg files, and the game will launch with it normally from the Blood settings menu (save and play blood).

So I'm not sure what's going on with that? I didn't have this issue last time I had Blood installed with bmouse on it.

did you change your dosboxBlood_single.conf file? You will want to change the line calling blood.exe to something like

BMOUSE.EXE LAUNCH BLOOD.EXE -ini dw.ini

I have my dosboxblood.conf set here:
[autoexec]
# Lines in this section will be run at startup.

@ECHO OFF
mount C ".."
c:
imgmount D game.ins -t iso
cls
bmouse.exe
blood.exe
exit

Should I change the two exe lines to "BMOUSE.EXE LAUNCH BLOOD.EXE?"

And Deathwish isn't the issue, the Deathwish shortcut actually works fine and boots with bmouse and works. It's the base game!

The target for the shortcut supplied with GOG is:

"C:\GOG Games\One Unit Whole Blood\DOSBOX\DOSBox.exe" -conf "..\dosboxBlood.conf" -conf "..\dosboxBlood_single.conf" -noconsole -c exit

What should I change it to? (using my install path)

just the two lines:
bmouse.exe
blood.exe

change that to: bmouse.exe launch blood.exe

Ah okay, thank you! works.