Ooh, now we're talking!
Just for the record, you can't "edit" DLL files, they are compiled binary blobs just like MDL and BSP. You gotta obtain the source code that these DLLs result in compiling.
You can use Solokiller's HL OpFor SDK: https://github.com/SamVanheer/halflife-op4-updated
Hostile Barneys can be a copy-pasted Barney with a single line of code changed, or you can add a map property to
(or to all NPCs) to make them change their classification (friend vs. foe).
DMC/Quake-style ammo is really just looking at the Tau cannon or gluon gun code, they have no reloading just like in Quake. Identify which parts of the code are responsible for that, and apply them to your weapon(s).
Red HUD colour is easy, simply change the hex colour value here: https://github.com/SamVanheer/halflife-op4-updated/blob/236e77682f1a2c147eab794b47880329e50b5011/dlls/cdll_dll.h#L204
Here are some example values: https://github.com/SamVanheer/halflife-op4-updated/blob/236e77682f1a2c147eab794b47880329e50b5011/cl_dll/hud.h#L25-L27
is pure red (255,0,0) and so on.
As for scientists that cower away from you, I think it is possible to alter their classification table so that they're always afraid of the player, i.e. treat the player as an alien. There's a whole classification mechanism in Half-Life's AI system where some NPCs see other NPCs as predators, or prey, or they mean nothing to them, and so on.
I'm not sure about boss fights, because that can mean literally anything. For all I know, I could be fighting a worm in a goldfish container (reference to sc_toonrun). You can set those up as a combination of a sequence of triggers and stuff, plus a special entity that sends fireballs at you (doesn't even have to be an NPC depending on what kinda boss it is), but of course, that will require knowing entity programming.
If you have questions (which you probably certainly do), feel free to ask. Are you looking for a programmer to do this for you, or do you wanna try and learn how to?