I have a PRS SE custom semi hollow. It's nice to play, but compared to my American PRS, it's lacking a lot in quality.

I don't know jack squat about pickups, or what ones to look at to get sounds I'm after etc and so on. I thought about getting some hollowbody 2 PRS pickups, but I'm sure there's better for cheaper.

Basically what should I look into for a nice warm clean blues, and good clarity when given a medium amount of gain, so I can play open chords with gain and get a non muddy sound like I currently get. And importantly, the stock pups are zebra cream and black humbuckers, I'd like to keep that look so the guitar looks factory spec.

Seymour Duncan Seth Lover
GFS Fat Pat
2002 PRS CE22
2013 G&L ASAT Deluxe
2009 Epiphone G-400 (SH-4)
Marshall JCM2000 DSL100
Krank 1980 Jr 20watt
Krank Rev 4x12 (eminence V12)
GFS Greenie/Digitech Bad Monkey
Morley Bad Horsie 2
MXR Smart Gate
What you want is a slightly brighter take on the standard PAF construction. It may sound a little thinner clean, but it's the only way you'll keep any clarity once you knock your gain past 2, let alone beyond. That's the unfortunate problem with semi-hollows, you either get a smooth clean and muddy overdrive or thin clean and clear overdrive.

There's not too much you can do about the tone as the stock pickups are already medium-wound with A5 magnets and mismatched coils. You can only get more clarity if you take on a weaker pickup. This should be fine for you if you aren't relying on pickup output to drive your amp, but still, just be aware that you're going to get a drop in output.

Try a Seymour Duncan Pearly Gates in the bridge and Alnico II Pro in the neck. They're just a tiny, tiny bit clearer and tighter than your typical PAF copies. The SD '59 and Jazz are similar winds with the A2 magnets swapped for A5s, which will give you even more clarity. All four of these are cooler than your stock pickups.
Also consider hum-sized P-90s, like the SD Phat Cat or Tonerider Rebel 90s. They will hum but they are much clearer and articulate than any humbucker can be. Depending on the volume you play at and how much preamp gain you use, the trade-off may be worth it.

You should also try simply lowering your stock pickups. The further they go from the strings the more sensitive they get, you get a clearer sound and in some cases improved sustain. Playing with the height of your pickups costs nothing, takes just a couple of minutes to try out and may be all your need.

What I'd really recommend though is you get in touch with custom pickup makers in your region. Sometimes local builders will be able to offer you a custom set of pickups for no more than a set of production Seymour Duncan or DiMarzio pickups would cost. The main advantage of getting something custom wound would be that they're almost always scatterwound, which gives you much better clarity. Have a search for what's near to you and see.
Yes, I know everything. No, I can't play worth a damn.
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Thanks mrfibble for the comprehensive suggestions. Appreciate it.

All my gain is off the floor, so I'm not driving my tubes very hard. Ill mess around with pickup heights and give that a go, interesting about lowering the, for sensitivity? I would have though they'd loose out the further from the strings they are.

In New Zealand there aren't a lot of custom guitar shops/ luithers to get to make pickups so I'm stuck buying whatever I can find/import. Hopefully I don't need to spend too much, as some gigs I defintly don't want to bring the American PRS to.