You can use almost any common diode for D2 (like LL4148, M2, S1A etc). It’s just for reverse polarity protection. Although the package size is SOD123, it fits most small SMD diodes, like SMA, MiniMelf, or you can simply solder a through-hole diode there too).
The 2×6 male/female pin headers are the most common 0.1″ pitch dual row male/female header. If you have a 2×40 or any thing that’s larger than 2×6, you can cut/clip it to 2×6.