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That is quite easy: I just added the line shuffle=NBRQ . That causes all of the mentioned pieces to be randomly permuted over their initial positions. (Only when you press the Restart button of the AI, though; the initial Diagram always shows the 'nominal' position, which might be important for knowing what the castling partners are.)

Since this isn't really a shuffle but a placement game, you did not specify any restrictions on the shuffle, assuming that the common sense of the players would avoid undesirable positions (such as all your Bishops on the same shade, or an unprotected black piece attacked by white). A random shuffle of course ignores such considerations. A rule like 'no unprotected attacked pieces' would be too complex to enforce anyway. But people can always reshuffle if a position comes up they consider defective.

If you post in HTML, please take care that your Comment contains as many </div> as <div> tags. Otherwise it would mess up the remainder of the command list. I had to add an extra </div>, because all other Comments were appearing inside yours! (It could be worse; I have seen cases where unbalanced tags made the entire remainder of the list disappear, including the link to edit the offending post, which made it really hard to recover from that.)

The way you formulated

Pawns and Kings are the only pieces that remain in their own half of the board in Version 2 of the game. 

implies that all other pieces have to be put on the opponent half, which is of course not true. The sentence seems redundant anyway; you already stated that K and P have fixed positions, and readers are not so stupid that they would have to be told the positions in which the Diagram shows them are on their own half.