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Comments

 There are some words which are already inflected, since they have
 irregular forms.  How do I write rules with multiple inflections,
 which case take these as input partway through the inflection?  Or do
 I just write a fully inflected form for them?  The example I have is
 snake, for which the plural form seems to be irregular.  After the
 plural form however, I could let it inflect for case following the
 normal rules.

You can't, with the LKB morphophonology rules.  But, you shouldn't
really try.  You should assume that some preprocessor is handling the
phonological irregularities, and handing you regularized forms.

 There are some sentences where both the subject and object are in
 nominative case.  I'm not sure what the rules are which determine
 which case should be used.  The lexical rules are currently written so
 that verbs take a nominative and accusative noun, but this will have
 to be revised to make it much more open.  How can I control
 overgeneration in this case?  What are some strategies?

I'm not sure what you mean by lexical "rules" here --- it's the
lexical types (for verbs) that are controlling the cases required of
their arguments.  As to how to handle double nominative sentences, it
depends on what the generalizations are.  Are there particular verbs
that take this pattern?  If so, you're talking about a lexical type.
Is it a construction with a specific meaning?  If so, you're probably
talking about a lexical rule (which applies to verbs and changes the
case required of the object) or a phrase structure rule.

noun-number-lex-rule := add-only-no-ccont-ltol-rule & 
    [ DTR common-noun-lex,
      INFLECTED - ].

I think it would be cleaner to put [ INFLECTED - ] on common-noun-lex.
Otherwise, I suspect the completely uninflected nouns are being allowed
as daughters...  And they're not, but that's only because you're putting
[ INFLECTED - ] directly on the lexical entries.

 My test cases only include examples of transitive verbs, so I wrote
 the lexical rule as
 trans-verb-tense-lex-rule :=
	lexeme-to-word-rule &
	[DTR transitive-verb-lex].

I'd be surprised if intransitive verbs (and ditransitives, etc) each
had different tense inflections.  Why not just use verb-lex for the DTR?