Mode A and B differences as I can see it is the pulse spacing (Mode A 8 micro seconds, Mode B 17 micro seconds) that's between the first interrogation pulse (P1) and the second interrogation pulse (P2)
For info Mode C has 21 microsecond pulse spacing and Mode D 25 microseconds.
As mode S is backwards compatable with all the other modes I'd suggest Mode B transponders could slot into the place of a Mode A one (same interrogation and reply frequencies).
Mode D i've got as not used and unassigned (think this is still the case?)
Mode S - yes you still need to enter the Squawk code manually. It's normally either a dial (as per Most mode A's) or a numerical keypad with display.