Which version of WFRP would you be running (there are 4)? 1E (which TEW was originally written for) is a bit clunky but works.
2E takes 1E and systemizes it a bit. Works a bit better, but I think loses some of the original charm. You can run 1E adventures with 2E with virtually no changes.
3E is radically different, using different types and shapes of dice, cards and tokens. It actually works pretty well, but all the bits can get in the way. Would definitely require conversion.
4E is the newest version, and shares the percentile dice of 1E/2E, but with significant tweaks as to how success is mesured, damage is applied, etc. I really like it (it's my favourite edition of my favourite game), but I admit that the rules are not a model of clarity. On Reddit, there is a group dedicated to WFRP, and some FAQs that might help you understand the rules. There is a new, expanded version of the TEW being released by Cubicle7.
BRP/RQ/CoC is a pretty good suggestion if you abosulutely hate any of the WFRP rulesets.
If you were going to use 5E (which I I like, but not for TEW), this is what I would do. The WFRP setting is definitely less heroic than your average D&D setting. Combat is dangerous and brings long-lasting consequences. Characters can become powerful (at least relative to other people), but they aren't superheroes. The setting has a 15th-16th Century level of technology (albeit with anachronistic steam technology) - not medieval like most D&D:
*Cap PCs at level 5 or 6, and use super-slow advancement. (You might even break each level down into "sub-levels", where they get individual features or bonuses from their class just to keep things fresh).
*All spellcasting is risky - all wizards should be forced to rule on the wild magic sorcerer random magic table. (There are no sorcerer or warlock character classes - at least for PCs). There might be some good 3rd party supplements that flesh out the random magic effects
*Use sanity/madness rules from the DMG
*Use the gritty realism rules from the DMG
*Use firearms/explosive rules from the DMG
*I would use the lingering injury and massive damage rules from the DMG
*I would consider using the speed factor and hitting cover rules from the DMG
*Character's standing in the world is determined mostly by their background, not their class. Background is a minor feature in most 5E games, but for the TEW it will continue to be important.
*Use currency and equipment lists from WFRP rather than the 5E - this will do a lot for players to feel that they are not in a standard D&D setting. In fact, rather than start PCs with the standard 100 gp, I would get players to find the WFRP career that most closely matches their 5E class/Background combination, and have them start with the set of trappings listed for that career.
My group is on board to play one of the most celebrated published campaigns of all time "The Enemy Within" for Warhammer Fantasy RPG. The problem is that try as I might (as a veteran of many game systems) I can't get the hang of the rules (even after reading over the rules for 9+ months). And where I do understand them, they are cumbersome and terrible, putting D&D 4e to shame, IMO.
With all the talk of Bait and Switch, how terrible would it be to run the campaign in a more familiar system (D&D)?