My one and only Strat is a 2003 MIM that I've done numerous upgrades to. The only original part is the body (sage green color). Its appointments are as follows:

1. Calaham (steel) tremolo block and base plate.
2. Graphtech block style saddles.
3. Kinman noiseless pickups (all three) with wiring harness.
4. Aftermarket pick guard ('can't remember the brand).
5. Fender (tapered) locking tuners (no string tree required).
8. Custom built (highly flame maple neck/12" radius maple fretboard).*

These appointments (especially the new neck/fretboard) have made a significant improvement in tone and playability of this guitar (to a point).

Here's the problem. All is well until I bend notes on the high "E" string above the 12th fret. I do some pretty large bends and those higher (bent) notes on the high "E" string seem to "fade"/wash out when I do upward bends/vibrato. It's not as noticeable on the bridge pickup as it is on the other two. The new neck/fretboard is slightly wider at the nut than the stock neck was. With this setup, the strings (in a resting state) sit directly over each pole piece on all 3 pickups. I can compensate a little by using an upstroke pick attack on those higher "E" string (bent) notes, but that can be a little disruptive in certain situations.

Is this a common phenomenon with a bigger neck/fretboard, or do I need to tweak my (pickup) setup?

*Thick, almost "U" shaped.