I think you missed my point about the cable and wiring. If you have phasing issues, it will be in the wiring or the pickups, period. This can include a guitar cable that has been wired out of phase, and you may not even know it. Just your pickups you might have a coil in reverse mode from the other, especially if you did split coil with a push-pull or anything, that is easy to do.
Also, in a studio, you don't usually grab a mic and start trying to fix a harshness that a guitar or amp is producing. You would usually hand the guitar player another guitar out of the ones there at the studio and fix the issue at the source. If you are trying to fix an issue that is not where it is happening then you are just masking the real issue and or making another part of the instrument worse than it could be. Like rolling of mid-highs or using a mic in a position that puts it a little out of phase, which can cause some issues later in a mix.
If you are just having issues with harsh frequencies that is what we have been discussing with this thread and I think a pickup swap would be what I would recommend. If you want smooth with superstrat, try some Dimarzio pickups. Something more balanced and not a whole bunch of high end, since it sounds like your guitar is just naturally bright. Don't put he JB in it, it will be horrible. The JB is not a great pickup in naturally brighter guitars. Darker guitars, like LP Customs (no maple cap) are perfect for the JB, as a for instance.
This pickup is pretty balanced and does not have a lot of high-mids, but a good bit of highs:
https://www.dimarzio.com/pickups/vintage-output/ej-custom-neck
Another good one, just has a bunch of high end chopped off, but will cut through a mix nicely.
https://www.dimarzio.com/pickups/high-power/illuminator-bridge
Another good one, for a bright guitar:
https://www.dimarzio.com/pickups/high-power/super-2
I have a feeling if you are not having phasing issues, and just frequencies that pop out and make things harsh, then the pickup saw is the way forward. If you are actually having phase issues as you mentioned before, then you need to find where you have a wire or two swapped for ground or flipped. Doing 50s wiring on a super-strat is not what I would attempt, personally since it was never really made for that sort of thing. The 50s wiring was made for guitars with 2 tone and 2 volume to make sure the ground was good throughout the whole circuit and in one quick shot. when you can't really make the circle with your ground wire, you know it is not really the right thing.
I am sure this is not what you want to hear, but those are both things that I think will fix your issue. 1) Find your phase issue, if you are having true out of phase and in phase with 1 guitar and IR loaded. 2) Fix your frequency peaks that are causing harshness. This I have a feeling will be a pickup swap (you can try 250K pots, but you will lose a ton of high-end that will be hard to add back later and might make the guitar dull or not pop out of a mix enough). Go with pickups that are more balanced and either roll off high or high-mids some and still very balanced.