Well FWE pretty much covers the first three things you want. Just be sure to use http://www.fallout3nexus.com/downloads/file.php?id=4968 for compatibility with WMK. There's plenty of settings for FWE that you can set to make the game more hard-core, setting the rarity of ammo and chems for example. And yes, FWE also has options to increase the difficulty and lethality of combat, your skills and the condition of your weapons will matter.
There's also http://www.gamesas.com/index.php?/topic/1160547-relz-arwens-realism-tweaks-thread-no12/ for another ovehaul. I (shame on me) have yet to use it but from reading your skills will matter when using firearms. Also has a few different optional modules that set out to make life in the wasteland harsher. Unsure about compatibility with WMK, maybe some one could chime in on that.
I haven't used it but I suppose http://www.fallout3nexus.com/downloads/file.php?id=1745 would be the go-to one for more chems. Not sure of any others.
http://www.fallout3nexus.com/downloads/file.php?id=8886 for stability.
Oh and if you decide to use EVE with FWE be sure to grab the following patches.
http://www.megaupload.com/?d=NG1YEAHI
and a fix for Pulse weapons...
http://www.megaupload.com/?d=752S4RMQ