Gary F,
To answer your questions:
Classical first-order
logic, usually abbreviated FOL, has pride of place among the open-ended
variety of logics that have been specified during the past century. 
Primary reason:  FOL is sufficient to specify 99.99% of all versions of
mathematics from ancient times to the present.  FOL can be used to specify
every digital computer ever built and every program that runs on any
digital computer.  And the syntax and semantics of any other versions of
logic can be specified by mathematical theories expressed in
FOL.
When I say that people in ancient times used FOL to specify
mathematics, I mean that they used the equivalent of the words AND,  OR,
NOT, IF, SOME, EVERY, and EQUALS (=) in a way that could be translated to
any modern notation for FOL, including eg1911. 
(http://jfsowa.com/peirce/eg1911.pdf )
Re Peirce's many versions of
logic:  Peirce made some extensions to Boolean logic in the 1860s, but his
major extension beyond Boolean logic was his logic of 1870, which went
beyond monadic predicates to n-adic predicates for any n>1.  De Morgan
called that work the greatest advance in logic since Aristotle.  And he
was right.
The discovery of complete notations for FOL by Frege
(1879) and Peirce (1885) presented mathematicians with a logic that was
sufficient to specify all of mathematics.   That was a revolutionary
advance.  Peirce (1885) also specified a version of second-order logic. 
That was an important advance beyoind Frege (1879). (See
http://jfsowa.com/peirce/putnam.htm )
Peirce also used logic as a
metalanguage in his 1898 example of an existential graph that stated
"That you are a good girl is much to be wished".  These two
additions (second-order logic and metalanguage) could be added to the
eg1911 notation with the same or similar additions he used with the
earlier versions of EGs.
The semantics of those additions could be
specified along the same lines as modern extensions to the algebraic
notations.  One version I have been using is called Common Logic (CL). 
For references and discussion, see the slides I presented at a conference
in June:  http://jfsowa.com/talks/eswc.pdf 
Re modal logic:  Any of
the notations for modal logic that Peirce introduced before 1911 could be
added to the notation of eg1911.  But Peirce himself was unsatisfied with
them.  He mentioned a replacement, which he called Delta graphs.  But so
far, nobody has found any MSS that specify any detail.  But any extensions
during the past century could be added to the notation of eg1911.  For
some discussion, see http://jfsowa.com/pubs/5qelogic.pdf .
Re
three-valued logic:  Peirce specified truth tables for three-valued logics
in some MSS.  Those could be used with the notation of eg1911.  But the
fact that he presented eg1911 at the beginning of a long letter on
probabilty suggests that he may have been thinking of probabilty as the
way to handle uncertain information.  If so, classical FOL, as expressed
in any notation including eg1911, could be used to reason about
probabilities.
Unless and until any MSS after 1911 are discovered,
nobody knows exactly how Peirce would have extended EGs to handle any of
the above issues.  But eg1911 is a *better* foundation for adding such
extensions than any previous version:
1.  The use of shading instead
of cuts or scrolls supports a simple extension beyond a two dimensional
sheet:  just use shaded regions in N-dimensional space.  In one of his
MSS, Peirce explicitly said that selectives are necessary only for a 2-D
sheet, and that EGs on a plane should be considered *projections* from 3-D
graphs.
2.  The drastic reduction in technical terms in eg1911
clears the way for further extensions.  In L231, he mentioned
"stereoscopic moving images" and regretted that he could not
afford the technology.  Today's virtual reality would be ideal for
allowing anyone to wander through a moving 3-D graph and make dynamic
changes to it.
3.  With today's technology, it's also possible to
include arbitrary images and even 3-d virtual reality inside any region of
an EG.  In a talk I presented at an APA conference in 2015 and later at an
EG workshop in Bogota, I proposed two new rules of inference --
observation and imagination -- which could be added to multi-dimensional
EGs.  Those two rules would be special cases of the rules of iteration and
deiteration.  For the slides, see http://jfsowa.com/talks/ppe.pdf .  Slide
2 of ppe.pdf includes the URL of a 78-page article that was published in
the Journal of Applied Logics,
John
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