Looks like you've got a fair bit of info to sift through here already (was weird to see this thread back in the new posts) I'm really not and expert with wiring either, but my understanding is improving every time I look at it.
The cap values as others have mentioned seem correct, but I'm just thinking.... I'm not sure I had tone control on the humbucker the way I wired mine. I am pretty sure I used a standard strat diagram as I cooked everything the first time I tired and got new pots and started again....was a while ago now. I never had any real complaints about it either, so I wonder if that's where some of the muddyness comes from?
So you could use .047uf for both tone controls and just have them wired for the neck and middle, and just have the humbucker go through the volume, might give it a bit more punch as the kit ones aren't especially hot wound.
That way you could use 2 250k tone pots and a 250k volume, which would make it all pretty bright.







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