I have multiple of these in guitars right now, and am a huge fan of both.
For a "Frankie" I'd go with the Custom. You'll get a lot of mileage from it that you won't need to get from a pedal or the amp. That said, it wouldn't be my go to...but it is the right "style" if somewhat overly hot.
The Custom is a serious metal pickup. It is often described as a "PAF on steroids" and that is true. I'd say it is way more than steroids though...It has a fundamental PAF character about it. Good bass, scoop-ish mids, and a clear high end. We can debate perception of the the mids as scooped or not as present as the bass and highs. It definitely has mids about it. The bass is tight and has a "Thump" factor. If you need bottom in your sound, this is the pickup you want. The highs scream as any 17k or so ceramic pickup would. They may/may not be juicy enough for your Frankie goals.
The Distortion is a full-on Metal pickup. I might play a lot of rock/hard rock with a Custom, but the Distortion really leans into the metal zone. It has nothing to do with a PAF sound. The bass is tight and notably less than a Custom. The mids are very present, and a little towards the higher side vs low mids. The highs are the same as the Custom. 17k or so ceramic screamer. The mids+highs really makes the Distortion scream and bass + mids gives it a chunk that is tight and super crunchy.
I think of the Custom as Def Leppard/Iron Maiden, and the Distortion as Judas Priest/Metallica, if that helps.
custom/59 Hybrid might be a better choice that is hotter, but not over the top. Of course, there is a volume knob. You could get a lot of mileage out of the right taper to roll off a touch of highs for that VH sound if that's what you want.
There are a number of pickups that ARE the same wind, with different Magnets. The Distortion and JB are NOT that. However - the Custom and the Custom Custom are! So...if you want even more EVH tone, on a FLoyded Frankie, get the Custom, try it. If you don't like it, swap the mag to an A2 from Ceramic. Then you have a Custom Custom...very popular around "1984" if you know what I mean...