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OK, it is a good idea to use Shatranj as basis, because that already has Pawns without double step, a Ferz as Queen, and no castling. The trick here is to consider the black and the white Elephant as different piece types (just as internally Fairy-Max considers white and black Pawns as different piece types). So there are 'upstream' Elephants, which will be indicated by 'B', and 'downstream' Elephants, indicated by 'E'. Then in the initial position I give white upstream Elephants, and black downstream Elephants. So I change the lines for b and e (like you already figured). I guessed a value of 300 for them; you probably know better what they are worth compared to a Knight. I make this descripton replace that for variant 'fairy', though, not shatranj, for reasons that will become clear below:

// Makruk (Thai Chess), sort of
Game: fairy
8x8
6 4 5 3 7 5 4 6
6 4 8 3 7 8 4 6
p:100 -16,6 -15,5 -17,5 
p:100 16,6 15,5 17,5
k:-1  1,7 16,7 15,7 17,7 -1,7 -16,7 -15,7 -17,7
n:450 14,7 31,7 33,7 18,7 -14,7 -31,7 -33,7 -18,7
b:300 15,7 17,7 -15,7 -17,7 -16,7
R:630 1,3 16,3 -1,3 -16,3
q:180 15,7 17,7 -15,7 -17,7
e:300 15,7 17,7 -15,7 -17,7 16,7
f:180 15,7 17,7 -15,7 -17,7

Now the initial position is not quite what it should be, as Fairy-Max always assumes Pawns on the second rank. So you would have to play from a setup position. To do this, make a file named makruk.fen that contains the text:

rneqkenr/8/pppppppp/8/8/PPPPPPPP/8/RNBQKBNR w 0 1

which is the FEN for the initial Makruk position. In variant fairy WinBoard will accept all pieces in FEN diagrams, while in Shatranj it would only have accepted KQRBNP. To play Makruk, you now would have to type in the 'engine' field of the startup dialog of WinBoard

fmax /fd=..\Fairy-Max /variant=fairy /lpf=makruk.fen /testLegality=false

(lpf stands for loadPositionFile.) The first two can already be selected in the combo box, you could type the other options behind it before pressing OK. You can also add this line in the file winboard.ini, replacing the 'fmax' line that is there now in the list of /firstChessProgramNames, or adding it below it, so that you can automatically select it from the combobox of the startup menu.

This is currently as far as you can get. It is not perfect: I see that Makruk has deviating promotion rules, and there is no way to tell that to Fairy-Max through the configuration file. Another, minor annoyance is that the appearence of the Elephant piece is different for black (Elephant symbol) and white (Bishop symbol). I really should fix Fairy-Max to automatically use the mirror images of all pieces for the opposite colors, so that the Elephants could have been programmed as the same piece.