I have built two 335 style guitars - the first was for a guy who plays mostly classic rock and I used the StewMac Golden Era pups. He is very happy with them with a fair amount of overdrive.
The second was for a local jazz player and he specified the Seymor Duncan Benedito humbucker. They are quite a bit more money and only come in a couple of colors, but they are the warmest lushest sounding pups that I have ever heard. He plays clean thru a boutique amp and again, he is a jazz player (all those wonderful major 6ths and 13ths and stuff).
I liked the SD Beneditos so much that when I built my L5 clone, thats what I used. That guitar is forcing me to learn all those wonderful major 6ths and 13ths and stuff LOL.
I'll make a couple of other suggestions about 335 style guitars. Consider putting some sort of terminals or other disconnect in the pickup cavities so if you ever decide to change a pup you won't have to fish all the wires out thru the f-hole. I actually did the wiring while the back was off and pushed it all inside with some little fish strings to pull it back out the holes. If you look at the bridge pickup cavity you will see the terminal strips for the pups and there is a little piece of string (actually dental floss) on each control that I could pull it out with.
And here is the inside with the wiring just sort of hanging there. I masked off all the holes from the inside, stuck the pieces of dental floss thru and tied a knot on the outside. After the finish was all on and buffed I pulled the masking tape using some dental tools, pulled on the floss and, presto, guitar was wired.
Last comment - decide on your bridge and tailpiece before you set the neck - it might affect the angle. I used a stop bar on the rock and roll version, a Bigsby on the jazz one. Since there are different ways to do the center block you should decide on that in conjunction with the tailpiece.
