I find it very annoying that enemies fight at full strength and run at full speed even when grievously wounded. Are there any mods out there that apply some kind of penalty as you take health damage, such as strength or speed penalties? I hate it when someone I'm trying to kill runs away and escapes before I strike the deathblow.

OBSE certainly has the fuctionality to recognise body parts, I know many mods have altered this dynamic. Take a look at the Deadly Reflex mod - I'm not saying it contains this feature but it's a good place to start looking.

I have deadly reflex, but it unfortunately has no feature quite like this. I've been ghetto-rigging solutions where I set their speed and athletics to 1 as soon as they break and run away, but it's something of an immersion-breaker.

It sounds like what you're looking for is Locational Damage, and its optional Blood Retexture, if you as well think the standard Locational Damage blood is too pinkish.