SIF = Selective Identification Feature
IFF = Identification (or Identify) Friend or Foe

1) What are the differences, both conceptually and in actual practice,
if any, between SIF and IFF?

2) The answer to #1 above may make this question irrelevant, but in case it
doesn't: Why does only Mode 4 has an Identification Response (IR) but
Mode 1, 2, and 3/A doesn't?

SIF is basically a selective identification feature added to older IFF
systems.  Newer IFF systems have a SIF feature built in.  The SIF
system allows for the identification of individual aircraft rather
than just whether it is FoF.

The need for the IR is due to the cryptogrphic nature of mode 4.  It
takes multiple correcct responses from an aircraft before it will be
declared a friend.  The interogated aircraft will only send a friendly
response if the interogator craft is friendly as well.

The below is taken from: http://www.tpub.com/content/combat/14308/css/14308_102.htm

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Basic  IFF  Mark  X   is  the  oldest  IFF  system  still used  by 
friendly  nations.  It  can  reply  by  mode  only (codes  are  not 
available  from  the  transponder).  The basic  reply  for  modes  1 
and  3  is  a  single  pulse.  The response   for   mode   2   is  
two   pulses   spaced   16 microseconds (µs) apart. IDENT (I/P) and
emergency feature   are   available.   A   low-receiver-sensitivity
function is also available. IFF  Mark  X  (SIF)   has  a  selective 
identification feature  (SIF),  which  adds  reply  pulse  coding  to 
the basic   IFF   Mark   X   system,   allowing   operators   to
identify, track, and control friendly aircraft. The SIF was added to
basic IFF Mark X because the system had low  inherent  security  and 
did  not  allow  operators  to identify  individual  friendly 
aircraft     The  number  of codes available is 32 in mode 1; 4,096 in
mode 2; and 64 in mode 3. IDENT (I/P) and emergency features are also
available. IFF  Mark  X  (A)  is  essentially  the  same  as  IFF Mark
X (SIF) except that mode 3 provides 4096 codes has the SSR mode C
added.

This is in response to richardn-ga's comment: Thanks for the
explanation and the link. I now understand the difference between SIF
and IFF. However, I still don't fully understand the explanation to my
question #2. In mode 4, the transponder responds to an interrogation
and the response is either valid or invalid (or no respond), and
that's the IR. Isn't this the same with Mode 1, 2, and 3/A, or is
there something I'm missing?