Re: HSS pickups
You will get nothing but anecdotal (unverifiable and non-scientific) evidence that there is any downside to using RWRP for hum cancelling. That said, neck only and middle only are going to hum anyway, as will the a split JB only, so I don't see it as much of an issue.
If hum is an issue, go noiseless and split the middle when combining with a split JB. You can also split neck and middle for better (brighter) quack.
For noiseless operation, get an STK-S4M for the middle and in the neck get an STK-S6.
I'd put a DiMarzio Area 61 in the middle and a Dimarzio Injector Neck in the neck for that setup, personally. For best quack use an Area 67 in the middle. None of the Seymour Duncan offerings will give you better quack with a higher-than-vintage single in the neck than an Area 67, period.
With a standard 5-way you can split the bridge and middle for hum-cancellation in position 2.