I have used the EVH Frankenstein pickup extensively in a Northern Ash bodied Franky replica and to me it is the BEST pickup for EVH type tones - it's mid heavy, with a darker high end and high output. Dunno why the OP is experiencing what he is... What he's describing sounds way more like the Duncan '78, which I also have extensive experience with...
On another note, I have to wonder about whether EVH was really using low output pickups like he said. After all, he lied about almost everything early on in attempt to throw off his imitators. For sure in the Ibanez Destroyer he was using a 13K+ output Mighty Mite 1300 Distortion pickup in the bridge, which is hotter than a Dimarzio Super Distortion. He definitely experimented with the Super D as well in the Franky guitar and the Black/Yellow one. There are old pics of both guitars that prove this...
All my VH clips were recorded with 12K+ output pickups (mostly with the EVH Frankenstein pickup, which is a whopping 14.4K output!) and that allows you to get the legato stuff without getting mushy. While Ed's tone isn't modern thick, a big characteristic is how mid heavy it is, I really don't think it sounds that bright...
When I tried the Duncan '78, I liked it OK at first, but it is REALLY bright and it sounded weak to me because of the low output. An 8.7K output pickup just doesn't get it done IMO... Even Rockstah's best clips were using the Super D. To me the EVH Frankenstein pickup sounds way more like early VH to me than the low output Duncan '78, as well as the vintage Mighty Mite 1300 and the Super D. Personally, I would not recommend a low output pickup for early VH tone, I think the EVH Frankenstein is perfect for it, with the 1300 and Super D close seconds.
If the EVH Frankenstein sounds like the OP is saying in his guitar, there is either something wrong with it, it is positioned improperly in the guitar, wired wrong (which is pretty hard to do!) or he got a bum piece of Northern Ash... All IMO, of course...
Steve