I'd say use your volume knobs to get the sound you like in mid position, that's what they're there for. But yes, going to a lower output pickup will give you more bite in middle (and bridge) position.
This is completely normal, especially with the 59/JB combo, it's one of those weird things where the big bottom end of the 59 just overpowers the JB when they are both on. I've had them in 2 different Les Paul's and it's been pretty similar both times. When you said it's better as soon as you roll the neck volume to 9, I know your wiring is ok. Middle position on Les Paul's is tricky with higher output pickups, I find a lot of nice "middle tones" by turning both volumes down to about 5 and then just working the neck volume up for a warmer tone or vice Versa for a brighter tone. I've only found a few sets of pickups that I really like in the middle position with both volumes maxed, Seth Lovers (of course), the Pearly gates set is great for that too, Barekuckle mules and Abraxas and oddly enough in the higher output realm, the dreaded 498T and 490R combo are pretty decent too. Try lowering the bass side of the 59 a few turns, it will start to get better as you get some of the strong bass from the 59 dialed out.
You won't hear a difference with only changing to 450k pots, and in fact, if they are 10% tolerance pots, the 450k pots could even sound brighter (500 - 10% = 450. 450 + 10% = 490).
I would first adjust pickup heights even before volume changes, but yeah spending $120+ for different pickups when a few adjustments might fix it is premature.
I have not had that problem (at least to the extent you are describing) in the over 50 guitars that I own, even with those that have the same or similar pickups or even greater mismatches. But then, I always wire mine with independent volumes wiring. I can't tell from your photos how you have yours wired, but would assume you have dependent volumes wiring which can have that kind of effect.
See if this makes a difference:
Attach the hot/lead from each pup to the center lug of its respective vol pot and attach the output wire that goes to the switch to the first lug on the vol pot (the third lug is grounded to the back of the pot). The wire to the tone pot can attach to the middle lug if you want modern tone wiring, or to the first lug if you want 50's tone wiring.
Also I hope that was a misprint about your capacitor and that it is actually a .022 uf cap, not a .22 uf. (It is a .022 uf if there is a "223" printed on the side of the orange drop).
And while you're at it rewiring the pots, if the tone is too bright put in some 250k vol pots. You won't hear a difference with only changing to 450k pots, and in fact, if they are 10% tolerance pots, the 450k pots could even sound brighter (500 - 10% = 450. 450 + 10% = 490).
It depends on where you go, but most good places take the pots that end up falling out of their 10% range to sell as either 450k or 550k.
