Wow, lots of stuff to consider in this question... which is good. You sound like you know exactly what you want... atleast in the tone department. As far as the middle pickup goes... You can check out pretty much any of DiMarzios single coils... Maybe check out the YJM (Yngwie's signature singles) I'm not a fan of his but they might be along the lines of what you're looking for. The rail magnet "single coil" pickups are usually in a dual magnet form... essentially making them minibuckers. Which is what you said you didn't want. I'm not sure If I've ever seen a true single coil rail pickup. The best thing you can do for string spacing is to look up the factory specs for the guitar... or just measure the string spacing at the bridge... That should give you an idea of what spacing the pickups should be. You can probably find a chart somewhere on the internet that matches pickup string spacing with Bridge spacing.

As for the cosmetic issues... Blue and black would be a pretty cool scheme. If you're worried about your trem sticking out you can always save up just a tad more cash a few months down the line and get a black FR licensed trem to go on there. Since it's an Ibanez with a pickguard you could also balance the aestetics of the chrome trem with a mirror pickguard... and black knobs and tuners. That would look pretty sharp. Give it that... Steve Vai flair. I would go with metal knobs too... incase you were considering plastic knobs...

And for the tuners... I would go for these They have an 18:1 tuning ratio and they have an auto trim feature that automatically trims off excess string..... and they're only a few bucks more. So you're getting more bang for your buck. the Sperzel tuners that you linked are a 12:1 tuning ratio... which means they will have less accuracy when doing fine tuning. and also... IF for some reason the tuning rod slips just a little... the 18:1 tuners will detune a lot less than the 12:1 tuners.