Hmm.
I wonder about pickup covers. My Rebel Yells have the chrome etched ray gun design. It would be weird to have one pickup like that and one which is unmatched. So far, the best option seems to be to get a nailbomb for the bridge which would give me that bit more push / phatness on the bridge pickup. The Rebel Yell bridge pickup is set pretty high and it definitely has plenty of hair. The bass side of the neck pickup is pretty much flush with the pickup ring while the treble side is about 1 - 2 mm above the ring. The bridge pickup is about 1.5mm from the strings on the treble side and about 2mm from the strings on the bass side... I'd say that this is a pretty extreme adjustment.
If cash was not a problem at all, I'd have to say that the Riff Raff / Nailbomb combo would probably get me closer. Of course, the Rebel Yell neck is awesome so just swapping one pickup would be ideal. Perhaps I'd have have to get a nickel cover on the nailbomb and swap it with the Rebel Yell cover so that they'd still be matching? We'll see, I'm still going to try micing things up. Again, the cab may be accentuating these differences and if I can't hear them mic'd then they aren't such a huge deal.
I think what I'm going through right now is just a case of growing pains as a guitarist. When I got the Rebel Yells, I had my Dual Rectifier and they were a HUGE improvement over the stock pickups, ESPECIALLY since they sound so perfect with that amp. I absolutely love the rhythm tone of the Rebel Yell with that amp. The surgically tight bass of the pickup really tightens and reigns in the absolutely massive low end inherent to that amplifier.
When I switched to the Electra Dyne, that's when I noticed that a meatier and thicker bridge pickup would push the amp more, particuarly on the Vintage Lo mode, which is where I spend 80 - 90% of my time playing live. I rarely, if ever, shift onto vintage hi, and only usually for searing solos. The dynamic nature of the crunch tones is really quite perfect on Vintage Lo and I particularly enjoy the hairy clean to wicked and articulate crunch on the neck pickup. I just wish that the bridge pickup was thicker, and beefier. The accentuated mids and high mids almost sound honky with the Electra Dyne, ESPECIALLY at low volumes. Once I crank it it isn't such a problem except that the low end starts to really get huge and needs to be tempered. It's a really neat / musical amp but it's a bit odd in some ways as well. That being said, beside the warts, it's the most fun / responsive amp I've ever owned / played.
It's also those accentuated mids and high mids that make that pickup so perfect for the recto. The Rebel Yell contributes the very frequencies that a Recto needs to really shine. So, it's a tradeoff. The Godin LG works very well for that phatter and beefier crunch tone on the Electra DYne but it sounds not so stellar with the Recto. The LP is the other way but it is my number one guitar and the Electra DYne is my number one amp. I guess the important thing here is to find the middle ground.