What values should be initially assigned to Checkpoints for a new Genesis block?
You can generate several blocks and put (block_height, block_hash) pairs into the following field. Or just delete all of the checkingpoints : )

static Checkpoints::MapCheckpoints mapCheckpoints =
        boost::assign::map_list_of
        ( BLOCK_HEIGHT, uint256S("0xBLOCK_HASH"));


static const Checkpoints::CCheckpointData data = {
        &amp;mapCheckpoints,
       bitcoin-cli getblock [last checkpoint block], then get the unix time, // * UNIX timestamp of last checkpoint block
        Write a script to count?,   // * total number of transactions between genesis and last checkpoint
                    //   (the tx=... number in the SetBestChain debug.log lines)
        estimate_a_number     // * estimated number of transactions per day after checkpoint
    };