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Comments

 avan vannoo parses fine
 The inflection for the other 2 isn't working.
 The inflecting rules are not being applied to these cases, although I can
 create the verb, and inflect it for tense.

You're problem is right here:

 ; Inflection for question marker -oo or -ee suffix
 quest-verb-rule := infl-add-only-ltol-rule &
                   [DTR verb-lex, INFLECTED +] &
                   [SYNSEM.LOCAL.CONT.HOOK.INDEX.SF ques] .

This rule requires something that is verb-lex as its daughter,
precluding the application of any lexical rules in between.
Since it's a word-to-word rule, it should work just to say 
[INFLECTED +] and [HEAD verb] on the daughter.

 1. Implemented a lexical rule to add the nominal form to the verb in the
 embedded clause.  (I ended up with 3, since I wasn't sure how to write a case
 that included all the verb types while excluding other types.)

The trick is to create a supertype to the three verb rules that
you want, and then have that supertype be the value on the DTR
of the nominalizer rule.

    daraivar kaar etauttatx     kutataikala kanatau
    driver   car  take-PAST-NOM child-PL    see-PAST
    The children saw the driver take the car

Something's broken in the semantics for this one:  The MRS only
has the predicates from the embedded clause, which suggests
that something has an underconstrained RELS value.  In fact, it
must be these guys.  They should be no-ccont.

; Inflection for NOML marker, to indicate an embedded clause
nomnl1-verb-rule := infl-add-only-ltol-rule &
                   [DTR past-verb-rule] .

nomnl2-verb-rule := infl-add-only-ltol-rule &
                   [DTR pres-verb-rule] .

nomnl3-verb-rule := infl-add-only-ltol-rule &
                   [DTR futr-verb-rule] .

Furthermore, these aren't adding any constraints, so you're
going to get overgeneration.  For example, the verbs with -atx can
head matrix clauses in your grammar right now, which I suspect
you don't want.


 2. I created a lexical type for the imperative which contrains the 
 ; Imperative verbs
 ; constrain the head daughter to be form imp
 imp-verb-lex := imp-head-opt-subj-phrase & 
    [ HEAD-DTR.SYNSEM.LOCAL.CAT.HEAD.FORM imp ].

In the naming conventions "lex" is the suffix for lexical types,
so it is odd here on the type for a phrase structure rule.

 3. I wrote inflection rules for the 2 types of imperatives.  One is not
   inflected, and the other is.

 ; Lexical rule to mark the verb as an imperative form
 imp-verb-rule := infl-add-only-ltol-rule &
                   [ SYNSEM.LOCAL.CAT.HEAD.FORM imp,
                     INFLECTED - ] &
                   [ DTR verb-lex, INFLECTED -].

 imp-pol-verb-rule := infl-add-only-ltol-rule &
                   [ SYNSEM.LOCAL.CAT.HEAD.FORM imp-pol ] & 
                   [ DTR verb-lex, INFLECTED +].


I think you've confused the feature INFLECTED with the type
inflecting-lex-rule.  The former indicates whether the word has gone
through enough lexical rules to be fully-formed.  ([INFLECTED -]
corresponds to 'lexeme' and [INFLECTED +] corresponds to 'word').  The
latter indicates whether the rule involves any spelling change.
Assuming no further affixes attach after the -ka/-0 indicating
imperatives, they should both be lexeme-to-word rules, but
imp-verb-rule should be a constant-lex-rule while imp-pol-verb-rule
should be an inflecting lex rule.  If that's not clear, please
ask for clarification :-)

In addition, there are two further problems with your imperatives:

1. They don't constrain the SF, and so are not having any semantic
effect.
2. They don't constrain the subject to be second person (this
is why you're getting them all over the place).

It should be straightforward to have the imp-verb-rules constrain the
C-CONT.HOOK.INDEX.SF to imp and the
SUBJ...LOCAL.CONT.HOOK.INDEX.PNG.PER to second. You could even define
a supertype to the two rules which includes this information.