What's a "lexeme" in A-F syntax search (and how do I discover them)?

What's a "lexeme" in A-F syntax search?
I ask because A-F seem to have a variety of criteria for what constitutes an independent "lexeme." They also seem to be inconsistent. This can be problematic for searches based on "lexemes," as it is difficult to be sure whether one has tagged of the various "A-F lexemes" that cover the one word a researcher is looking for. For example, most people would hthink that the word "God" (אלהים) is just one "lexeme". I tried this and had problems, as documented in this thread. Those more aware of research in the field will realize that there is the theoretical possibility that אלהים is just one of three possible words for God (alongside אל and אלוה; though some think these are not separate "words" [lexemes?] but developments from the single root אל). Thus, they would tag these three "lexemes" when searching for "God."
A-F do in fact have these three separate "lexemes" for God. This would imply that "roots" define lexemes. However, rather than having three lexemes to cover the gloss "g/God", they have five! The "root" אל is sub-divided into two categories, אל 5and אל.7 and this is done, not according to the criterion of "root" but semantics: one means "god" and one means "God." I presume the idea is to have a separate tag not only for different roots with the same gloss, but also for the same root with different glosses (i.e. according to "lexical meaning"). But they aren't consistent here, as אלהים also has two different gloss: God or gods/heavenly beings. But A-F categorize it as a single "lexeme."
The fifth lexeme is אלה.5, and I can't explain what that is about. Theoretically it should be the same as אלוה, but this "lexeme" already has a separate tag. My problem: how can I be sure that I've tagged every single "A-F lexeme" so that it covers what in the dictionaries is a single lexeme?
The case of נָהָר (river, stream, current) shows that this is even more complicated (and seemingly inconsistent). A-F allocate what in the dictionaries a single root three lexemes. The first two are semantic: one for the meaning "river" and one for the meaning "stream" (but why not "current"?). The third introduces a new category and, as far as נָהָר is concerned, creates an entirely new entity that does not exist out side of A-F's classification system: morphology. נָהָר is masculine, with a masculine plural ending. Sometimes, however, the plural is feminine. This has nothing to do with a change in root or even semantics. Nevertheless, A-F decided to create an imaginary feminine singular form to parallel it: נהרה.1. I would thus have to know that they have done this, otherwise my search would not throw up hits such as Ps 24:10, in which the word is actually נָהָר, but just happens to have a feminine ending (they also tag it semantically as "river," though in Ps 24:10 it means "currents", which means that they'd have to have an extra נהרה to cover at least these two varieties of meaning).
I could understand the usefulness of this gender distinction for certain research purposes, but A-F aren't consistent here either. רוח (spirit, wind), for example, is usually feminine. It can, however, be masculine. A-F, however, don't have an extra tag for those instances in which רוח is masculine.
A-F do not have an entry in their glossary explaining what they mean by the term "lexeme."
I should also point out that this is not an issue of homographs. Homographs really are two different lexemes and anyone with a basic knowledge of Hebrew ought to be able to distinguish between them (e.g. את as "with" or as notae accusativae).
So, to summarize my two issues:
1) (theoretical) What is an "A-F lexeme"? and
2) (practical) How can I make sure I have all my bases covered when searching for what in most dictionaries counts as a single word?