Check this page http://www.midibox-shop.com/info.html to make sure you have the components mounted in the correct places. There is also a parts list for each module.
The holes in the middle may be for the SIL resistor modules, see the link above.
There are extra rows on the DIN modules so you can use SIP resistor networks or discrete resistors as pull-ups. There are drawings on SmashTV’s site that illustrate this. There is no advantage to using one over the other.
The 100 uF capacitor is a fairly recent addition. It’s C5 in this schematic.
I have made several MIDIbox projects with DOUTs and I have never used or needed this capacitor. You might, if your project uses a lot of high-current LEDs, or motors, or if it has a shitty power supply, or perhaps other reasons.
Others may disagree with me, but I would leave it out unless I needed it for some reason, especially since you’d probably have to solder it to the bottom of the board.