Does anybody know how long installing El Capitan onto a USB 2 pendrive from another USB 2 pendrive takes on a MacBook Air?
I've never done this before, but from the looks of it, the speeds will be limited by how fast your thumbdrives go.

If I remember correctly, an El Capitan install is around 8-10 GB in size, so the 16 GB one you're installing to should be sufficient.

USB 2.0 in reality can IO data at around 30-40 MB/s (although this depends on the make and model of your pendrive).

Using these factors we can calculate that an installation can take up to 6 hours for copying alone, not factoring the CPU overhead in installation.

Although 72 hours is a bit of a stretch, as long as your USBs remain flashing I would be fairly certain the system is doing something and not worry about it halting.