As someone who's just sold an Explorer after 12 years and tried a couple of different BKP sets in it I would say the following:
Out of the Nailbombs I ran the alnico one in the bridge and the matching neck, and I was pretty happy with that, especially compared to the alnico War Pig set that I had in it first. I had the same bridge pickup in an SG before that and hated it there, it was too hairy and aggressive in that guitar, but the Explorer mellowed it out quite a bit, although I still felt that the guitar lacked some cut and was quite bassy. But I had the pickup from being in the SG and figured I would give it a try. At first it was in D standard and then I tried B standard and C standard. D standard was fine, C standard was nearly as good, B standard a bit too low.
I always thought I could have done a lot better with that guitar if I had a bridge pickup that is much tighter in the lows with less low mids. I never tried the Cold Sweat bridge I have in that guitar, I guess I basically got sick of experimenting with it given that it was quite a big guitar with a big case and I ended up getting a super strat that could fit in my car easier with the stuff we take on interstate tours. The amp and cab I used with it was always a Peavey 6534+ and a V30s 412
The pickups I always wanted to try in it were:
Impulse
Rebel Yell
Emerald
I think any of these would be excellent in an Explorer and eradicate the muddy factor, while the inherent bassiness of the Explorer would ensure that it still had plenty of oomph. All of them are also better lead pickups than the NBs (and come with awesome matching necks for leads and cleans) and are awesome rhythm pickups. The Nailbomb set was nice but I think these three sets would all be superior, especially for lower tunings.