If I was going to do this in a quick and easy manner (and assuming you don't want subspecies), I would do the following:
1. Download the excel spreadsheet list for the most recent IOC list
2. Use the sort function on the breeding range column
3. Delete all the taxa that don't start with AF, the code for Africa at the beginning of the breeding range info.
4. Use the Sort command again, this time on the first column, which actually has a numerical listing of where the birds go in the taxonomic sequence. This will put things "back" the way they should, including grouping everything with the proper family, genus, and so forth
Downside is again I think the subspecies information would be hard to keep track of, so if you need this it's going to cause a problem. Also this list presumably wouldn't capture vagrants or species that have a presence but miniscule one in Africa. That might not be all that important for you, I don't know. Pelagic species relevant to Africa would begin with AO, IO, or SO, so you would need to either preserve them and edit out the non African species, or cut all of them and then add the relevant species back in.