If you look at the assembly manual, the 100nF cap next to the 8-pin connector on top is not supposed to be loaded. As for the 4k7. it looks like the posted BOM is in error. There are 4 on the board (pullup on ~MCLR, pullups for the pushbuttons, and the pullup for the clk out on the RTC). I guess we will have to wait for RJ on this. If you don't have an extra 4k7 resistor lying around, you can likely use anything from around 2K to 10k for the button pullups (the two to the left of the PIC)
/mike