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Comments:

 Although I created 2 forms of imperative, the different forms only
 caused overgeneration.  (Generation would create both the base
 imperative and the polite imperative.)

I imagine this was because there was no diference in the MRSs
they produced.

 The verb's object agreement was not completely correct.

"object agreement" is when the verb inflects depending on 
some property of its object.

 For Malayalam, the verb's object is marked as accusative if the
 object is sentient.  Otherwise, the object is in accusative case.

YM "in nominative case", right?

 The transitive verb rules were modified to require a case acc noun.
 Since the neuter nouns are case nom+acc, they can be objects.  The
 ANIM+ nouns can only be in the object position in the accusative case.

 kutatai ammaye villacu used to generate both nominative and
 accusative object forms, but now has been corrected to only generate
 accusative object forms.

Nice!

 1. Use INFLECTED: I declared INFLECTED - in all of my verb lexical
 entries.  Then the inflection rules were specified to require a
 daughter with INFLECTED -.  This was added to the question inflection,
 imperative inflection, and auxiliary verb inflection.

 The inflection rules of embedded verb, and negative inflection
 don't have the requirement of INFLECTED - since their inflections are
 added after other inflections on the verb.

Actually, INFLECTED is used to distinguish words that are *fully* inflected
(ready to go play in the syntax) from those that are still incomplete.
The syntax rules all say [INFLECTED +] on their daughters.  The lexical
rules all already do the right thing (copy up INFLECTED or change it from
- to +, according to the type).  All you probably needed to do was add
[INFLECTED -] to the lexical types (= lexical entries themselves).

 2. Use the MC feature:I added restrictions on the MC feature to my
 verb rules.  The question verb, and auxiliary verb are MC -.  The
 nominal forms, which are embedded have MC na.  (I'm still not really
 sure what the MC value is doing.  I have quite a variety of different
 settings which seem to work, but I'm not sure why.)

[MC +] means "matrix clause".  [MC -] means "embedded clause".  [MC na]
means "not eligible as is to be either matrix or embedded clause --- must
go through some other rule first."