First of all, if you think the pickup sounds like shit, take it out and sell it on Craigslist/eBay. If that's an active EMG (not EMG-HZ) with plenty of wire you could get about 40-55 bucks for it (maybe. I'm not sure). For knobs, get whatever is comfortable and looks good for you. It also looks like you need a switch. If I were you, I'd get a 5-way stratocaster switch (Fender brand), as they're really really easy to work with compared to the Ibanez/Jackson ones and they can do most common pickup configurations. For pickups, do whatever you want. I'd go with a single coil size Air Norton for the neck and for bridge, I might go with a Super Distortion, or an Evolution. I'm really happy with the Steve's Special but it might be worth it to try something else. Middle pickup might be an HS-2 or HS-3. I dunno, that's just me. That's something you have to research and decide by yourself. As for the finish, I personally have no idea. I was trying to figure out what I'd do in your situation, but I'm stumped as well. I'd probably just leave it how it is.