The black box is probably associated with the air injection system on a B13. There is a valve and a couple black boxes right in front of the valve cover. This system is critical to reducing emissions. In most states, you won't pass a tail pipe emissions test without it.
A header designed for an SR20DE should come with 3 fittings in the primary tubing: O2 sensor, EGR connector, and AIV pipe. Most come with plugs for the latter 2 in case you choose to run without them, or to install the header on a later model car that does not have the AIV.
I don't know what type of header you are looking at, but the SSAC is famous for not providing proper location and angle for fitting the hard EGR tube, poor location and fit for the AIV tube, and leaking at the EGR connection -- you can fix this last problem with washers but you need to be aware of it.
The other headers I've used on an SR20DE (Hot Shot and Topspeed) have fit like the people that built them gave a sh*t.