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In terms of just balancing the output, I've found the whole Custom line matches the neck P-Rail. Neck P-Rail series is a good output match for a Custom or Custom 5 in series, again they match when both pickups are wired parallel, and split the P-90 portion of the P-Rail will be just a tiny bit hotter than a Custom is split while the rail coil is just a tiny bit weaker than a split Custom. The bridge P-Rail is a bit weaker than the Custom line on paper, but I find the thick and bassy tone of the P-Rail makes it sound louder than the specification is, so the end result is it feels like it's around the Custom's level of output.
But in terms of EQ, as others have mentioned, the P-Rails are total opposites to the Custom line, at least in series, and really they're kind of opposite to all other Seymour Duncans I've tried. I've not found anything that matches tonally with a P-Rail neck in series, other than the P-Rail bridge, of course. I wish there was a more standard humbucker that had the P-Rails series EQ balance, getting that tone but with a traditional covered look would be a big help in several of my guitars. The P-Rail really is meant for people who mostly want a P-90 tone but some extra options on the side, as opposed to a standard humbucker where you're obviously prioritising the series tone and any split or parallel sounds are the bonus.
So I'd suggest you either use the P-Rails for both bridge and neck, or just give up on making the two positions even and just let the neck P-Rail be its extra-thick self and give the bridge its own, different tone. There's no regular humbucker that matches with the P-Rail neck very well. The 498T or Custom 5 will 'keep up' in terms of the volume, but tonally it'll be a mismatch. That isn't necessarily a bad thing.
Matching with a middle single coil is a bit easier. The SD Hot Stack (that's the one with the big bar, not the rod magnet Hot Stack Plus or the double-rail Hot Rails) matches the P-Rail in output and is tonally a nice match as it is just that little bit thicker and smoother than a regular single coil, though it is hum-cancelling on its own and I can never remember how to get it to also be hum-cancelling with a split humbucker (or P-Rail) as well. The Quarter Pound also blends nicely with the P-Rail, since again it's just got a little bit of extra smoothness and power, and that one isn't hum-cancelling by itself, so you could easily get it to be hum-cancelling with either the P-90 or rail coil of the P-Rail.
edit: don't worry about the control values. You can make each pickup 'see' its own control value by using a 500k pot and then wiring in another resistor to the single coil, so for example the two humbuckers/P-rails will work with the full 500k while the middle single will be getting 250k. Or, with those slightly smoother and thicker middle pickups like the Quarter Pound and Hot Stack (or Vintage Rails, Cool Rails, a Hot Rails wired parallel, etc etc) you can usually get away with just using 500k anyway, they won't get screechy like standard singles.
But in terms of EQ, as others have mentioned, the P-Rails are total opposites to the Custom line, at least in series, and really they're kind of opposite to all other Seymour Duncans I've tried. I've not found anything that matches tonally with a P-Rail neck in series, other than the P-Rail bridge, of course. I wish there was a more standard humbucker that had the P-Rails series EQ balance, getting that tone but with a traditional covered look would be a big help in several of my guitars. The P-Rail really is meant for people who mostly want a P-90 tone but some extra options on the side, as opposed to a standard humbucker where you're obviously prioritising the series tone and any split or parallel sounds are the bonus.
So I'd suggest you either use the P-Rails for both bridge and neck, or just give up on making the two positions even and just let the neck P-Rail be its extra-thick self and give the bridge its own, different tone. There's no regular humbucker that matches with the P-Rail neck very well. The 498T or Custom 5 will 'keep up' in terms of the volume, but tonally it'll be a mismatch. That isn't necessarily a bad thing.
Matching with a middle single coil is a bit easier. The SD Hot Stack (that's the one with the big bar, not the rod magnet Hot Stack Plus or the double-rail Hot Rails) matches the P-Rail in output and is tonally a nice match as it is just that little bit thicker and smoother than a regular single coil, though it is hum-cancelling on its own and I can never remember how to get it to also be hum-cancelling with a split humbucker (or P-Rail) as well. The Quarter Pound also blends nicely with the P-Rail, since again it's just got a little bit of extra smoothness and power, and that one isn't hum-cancelling by itself, so you could easily get it to be hum-cancelling with either the P-90 or rail coil of the P-Rail.
edit: don't worry about the control values. You can make each pickup 'see' its own control value by using a 500k pot and then wiring in another resistor to the single coil, so for example the two humbuckers/P-rails will work with the full 500k while the middle single will be getting 250k. Or, with those slightly smoother and thicker middle pickups like the Quarter Pound and Hot Stack (or Vintage Rails, Cool Rails, a Hot Rails wired parallel, etc etc) you can usually get away with just using 500k anyway, they won't get screechy like standard singles.
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