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Comments:

 Though ma: is a particle, its distribution is actually

... actually what?

Is there any meaning difference between la: and lam/lan?  It
sounds like you have a preverbal adverb strategy for negation.

 In addition, /wa/ can be used to coordinate nouns within a matrix
 clause. When this is done, agreement on the verb is shown not with
 dual inflection, as might be expected, but rather with number/gender
 that matches that of the first conjunct.

Cool :-)  The first conjunct would be the one closest to the verb,
wouldn't it?  Do you see number/gender agreement anywhere else in 
the language (e.g., with adjectives), and if so what happens with
coordinated N's?  What about coordinations involving conjuncts with
different person values?

 Finally, if the subjects of the coordinated phrases are coreferential,
 /wa/ may be left out entirely.

This sounds like apposition, not coordination.

 or X=Y, X!=Y meanings

What are X=Y X!=Y meanings?  This seems to be terminology from 
the online page, but you should try to translate into categories
we have been using and/or provide a description of what that means.
(From a quick look at the page, it looks like they're talking about
sentences with non-verbal predicates.  The = and != metaphor is
probably influenced by the fact that English uses the copula (forms
of 'be') in these predicates, even though Arabic does not always do so.)

 There is another form called the jussive, however, that is used in
 negative imperatives, and in other ways that I find only oblique
 references to, such as an apparant "permissive" construction with a
 preposition 'li'

	li		t-aktub
	pcpl	2SG-write
	'let him/her write'	

Example with a negative imperative?

 Regardless of the form of the modal element, the subordinated verb
 within a modal is formed using the subjunctive,

Even when the modality is expressed by an adverb?
Also, what is the word order with the auxiliaries.  Where do they
appear with respect to the subordinated verb?

 In finding a good transitive example, I also found a good example
 showcasing the VSO/SVO asymmetry that I referenced in my lab 1
 writeup.

 To recap, when the order of elements is SVO, the verb and subject
 agree in both number and gender, but when the order is VSO, the
 agreement is only in gender; the number of the verb is always
 singular.

This is cool.  It would have been helpful to paste the example into
your write up, so I could see what you are talking about.  Are there
constraints on when you get SVO versus VSO order?  Do you end up with
different forms of the verb?  Is the gender agreement handled by the
same affixes in both cases, or is it a different set of affixes (where
the number and gender information are expressed in single portmanteau
forms)?

 I was unable to find any specific examples for embedded declarative or
 interrogative clauses, though there were some offhand references to
 them in my grammar. The references seemed to indicate that such
 embedded clauses would be treated similarly to modals, but there was
 not enough information for me to build examples

We will be covering this in the class --- I'm pretty sure Arabic has this
phenomenon.  Have you found a native speaker yet?  You can probably get
at these by asking for translations of sentences with "think", "know" and
"ask" with clausal complements.

Btw, have you decided which variety of Arabic you're focusing on? MSA?
The spoken variety from any particular region?

Consider adding some ungrammatical examples for coordination of NPs
with extra "wa" markers and/or the "wa" in the wrong place.  (or no
"wa").

Are overt subjects with imperatives grammatical?

No ungrammatical examples for modals?

You should add some examples for case showing that the transitive verbs
require NOM ACC, not ACC NOM or ACC GEN or NOM NOM or ACC ACC...

 Source: {b}
 Vetted: {s}
 Judgement: {g}
 Phenomena: {case, agreement}
 qara?-a		?al-?awlad-u	d-dars-a
 read-3SG.MASC	the-boys-NOM	the-lesson-ACC
 'The boys read the lesson'

If this is grammatical, there's something wrong with your
glossing conventions, I think.  That is, it seems that -a
just counts as 3rd person masculine when the subject follows
the verb.  Even if it's the same affix as the 3SG.MASC form
in SVO sentences, I think the gloss should reflect what's happening
in this sentence.

Also, you say this series is illustrating case and agreement,
but I don't see what it has to do with case.  Maybe word order
and agreement would be a better combination of phenomena tags.