When you use FOMM, an entry under the tab "Tools" (called "Archive Invalidation", strangely enough) needs to be checked and then takes care of the issue.
Wrye Flash can do the same.
A merged patch will do just fine, just follow the instructions precisely – but you already know that.
If "realism" is your goal, FWE wasn't the best Overhaul you could have chosen. I am now using http://arwenevecom.ipage.com/Fallout/FO-mods04.htm for the first time instead of FWE and they turn the Wasteland into a more gritty experience. Among other modules, it incorporates a system to deal with injuries and needs that is more demanding than FWE+IMCN and, imo, adds a lot if you want to deal with the consequences of a life under those conditions.
Some other mods I like:
Armor & Weapons (and effects upon them):Advanced Recon Stealth Armor (plus the night vision and the trap detector)
DC Ranger Arsenal (armor, gear, weapons)
Dragonskin Tactical Outfit (one of the best "soldier" outfits)
Impervious Power Armour (makes a Power Armour wearer a tough nut to crack)
Powered Power Armor (adds upgrades to power armour; I rarely actually wear Power Armour at all but if I do, I want options, options, options)
RH_IronSights – FOSE (bundle it with http://www.marcurioscache.nl/?q=fo3tofps and some weapon-upgrade-mods and you are as close to a shooter as F3 will probably get. Most weapon mods linked on the IronSights page are also good)
Solar Scorcher (fun weapon)
Steiner Combat Gear (another good outfit for a soldier-like appearance)
Weapon Mod Kits (already on your list).
The world around youBA_WastelandRestoration (if you think that the flora should have already started to grow back 200 years after the war – GreenWorld, Greener World and Recovering Wasteland are alternatives, but not as good, imo.)
Fallout Street Lights (when you use Fellout, the night is dark and street lights a welcome aid)
Fellout
Ranger HQ (because it wasn't an HQ at all in vanilla)
TecVault (new home, must be earned)
The IMAGINATOR for FO3 - Visual Control Device (to control the light very precisely)
http://www.marcurioscache.nl/?q=fo3urwl (I've always liked the colours of URWL and the added weather script is comparatively fast. An alternative to Fellout and Weather mods).
Quests, adventures, new landsA Quest for Heaven (a quest that consists of several parts)
Cube Experimental (maybe not lore-friendly but well done)
MarkB50K Wasteland Patrols (What, you don't want more enemies?)
Project Genesis
http://www.fallout3nexus.com/modules/members/index.php?id=137055's quest mods have always been among my favourites
Real Time Settler
The Crimson Caravan v1.3 Beta (rich, but some annoying bugs)
and
Alton IL (new addition, looks very promising; will add it when my new character has matured a bit).
Enrich/improve the experienceDK Bullet Time (more "realistic" than VATS – I don't use it anyway)
FO3 to FPS (already mentioned - a more shooter-oriented experience. But since all modules can be used independently (the integrated versions of Bullet Time and Sprint work fine, for example), you can also use the mod to add aspects to a more "realistic" approach)
Karma Revamp Mod (because Karma in vanilla changes too rapidly)
Refurbish DLC (so that the DLCs are better integrated into the unfolding story)
See you – Time for Bed (the world continues to do its things while you are asleep)
Sprint Mod (running away fast might save you)
Zumbs Overhauled Real-Time Security (real-time lockpicking, hacking, and lock smashing).
And for a little added fun:Laurens Bathroom Poetry (adds graffiti, words of wit, and poetry to bathrooms)
Playing With Firepower (exotic weapon effects).
You can find all those mods easily on the Nexus, apart from the ones made by Marcurios; that's why they contain links.