Many of the proteins of P. falciparum are not annotated because they can't be annotated at present, not for the lack of trying. I don't mean to presume too much, but for a model organism such as this it is unlikely that most people will do a better job with annotation than what is already available. I am saying this to alert you that you may spend a good deal of time trying to annotate these proteins and have little or nothing to show for it.

Also, it depends on what annotating a protein means to you. Usually it means describing its molecular function (e.g., histone lysine methyltransferase), but sometimes even a general biological function will suffice (e.g., involved in cell division). Either way, your proposed strategy will take a long time and likely not work. More recent annotation tools work with databases of protein families such as Pfam. See here and here how to install it locally so you can test your proteins of interest. You may want to try a conserved domains search tool or install it for local use as described here.

Finally, you may want to try the HHpred server, but it is not easy to install it locally. I suggest you try the web interface first and decide if it is worth the effort.