One might argue that it doesn't matter which one you choose, you'll always wonder what the other choices would be like. The greener grass and all that. Add to that, no guitar is perfect, only varying degrees of almost right.
Assuming you'll build just one for now, I would recommend you get to some guitar stores and play an Explorer type, a Strat and a PRS and see how they feel to you. Make sure to try them standing and if you can with the strap you plan to use. Who knows, you may find you hate the Explorer once you're playing one. They look cool, but might not fit you and your style. Same with a Strat and A PRS. I used to have a real lust for Explorers myself until I actually played one. Didn't like it at all. Didn't fit me right. It hung funny and I hated the way it dug into my right rib.
Guitars are a very personal instrument, and since you plan on building one at least, you might as well stack the odds in your favor for the first build and try to come to terms that it won't be perfect, but it will be yours and you get to build more later.
Also, I do not adhere to the philosophy that certain guitars are better for any given type of music than any others. What matters is what feels most right for you. A player might adore Led Zep but can't stand to play a Les Paul for 45 minutes at a stretch. Maybe an SG works better due to it's lighter weight and you can still play Led Zep songs all night and be happy about it.
You can work all sorts of variables to get the tone you want; amp settings, guitar settings, effects, but it's hard to change the way any given instrument feels.
Finally, I understand perfectly the great fun of designing guitars. I got close to a dozen I want to build. Closing in on my first completed build and I can't help thinking about which one will be next. Design all you want. It's fun. They're always perfect until they become real.