Solutions to covering exposed pin headers using a cap

I think you'll find assembling it pretty straightforward when you have the bits in your hand. It's the 'now injection-mould the body' stage which comes next that you'll struggle with.

For a one off repair like this, you can probably do something useful with heatshrink to keep it all together.

Alternatively, cut an existing USB cable in half, and use the 'A' end with some of its attached cable. Then you'll only have to join the cables - another heatshrink job.

If this is for production access only, then here's a trick I used once. The PCB (standard 0.062" thickness) was designed with SMT pads along one edge (both sides) so that a 2×7 0.100" JTAG header could be soldered to it, with the pins sticking out from the edge. This was useful for debugging prototypes, which needed more or less constant access to the JTAG (and weren't in cases).

In production, the connector is omitted, and I used a slightly modified DIP clip to access the pads for the connector. I just needed to bend the contacts inward a bit to get adequate friction and contact pressure.

Instead of the DIP clip, you could use a standard card edge connector as well.