Ok I will stop starting each post with ok
I checked and tweaked the layout and this is the result
Basically the idea is to split the layout over two boards, connected vertically with stackable headers. The red pads are the points where the two boards are connected (the bottom board in the layout is placed under the top one). Instead of having a female type B usb plug I marked the traces you need to solder the USB wires to, so you can solder and hot glue a standard male USB cable instead.
I tried to keep everything in a 41x34 veroboard (that you split on line AA) that is the "big" board sold by Tayda.
By having CONN4 and S1 on a daughterboard you could avoid using wires on the bottom board and you could shrink the overall size of the completed board.
The names of the components on the layout match the schematic/PCB on the website, the GNDs are only for helping understand the wiring since you have to wire the USB cable only
BTW I have just discovered how easy it is to program AVRs with an Arduino and obviously you can program PICs too (even though it's not that straightforward) and that makes this layout even less useful and interesting, but I've already made it, so...