I have a jackson dinky with HSS setup.
I gonna switch the stock pups with seymour duncans.
I decided on a custom bridge, but idk what to put in the middle and neck.
Any suggestions?
I play more metal/rock, but a nice clean sound would be good.
Classic single coils or single coil sized humbuckers?
I was looking at a few. Anyone try a cool rails, little 59 or yngwie models YJM?
I have found the HSS-setup is a compromise that really isn't ideal. You have the humbucker for heavy distorted tones, and the single coils for cleans - in theory, but they are never volume matched so you can't really switch between them... I end up using half of the guitar, which takes away the whole idea of having more possible tones.

I have the Seymour Duncan JB Jr. in the bridge and neck position in my #1 Strat, and can recommend it. It cleans up well, and at least in a Strat it does not take away the character of the guitar or the single coils that it replaced, while still being a lot more output and volume.
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Apparently once also known as PonyFan #834553.
YJM's have a pretty low output so as mentioned alread there wll be a huge volume drop when you switch pups. i'd look at a Lace Sensor blue for the neck. won't have as big a volume drop and will match your other pickup better tone wise while still giving you the more stratty tone.