Given its only full-speed USB (12Mbps), the wiring is quite forgiving, so you can probably bodge something reasonably well.
I'd probably get a through-hole USB connector (same PN as the BOM for the V4.6). You could try placing the connector upside down in the same place and glue or solder the sides of the connector to the board.
Some hookup wire to the pins marked in the image on the diode D2 and on the PIC socket (probably drill a small hole through the board and solder on the bottom using something like magnet wire or other thin wire).
For the PIC programming, any programmer that claims to program a PIC18F14K50 should do the job. The hex file contains the program and various settings. A PICKit 2 clone would be best as that's what I use (will I use genuine one that I got way back, but a clone should work too).