// Check if bundled product already exists
$bundled_product_id = Mage::getModel("catalog/product")->getIdBySku($data['sku']);

// Load new bundled item
$new_bundled_item_id = (int)Mage::getModel("catalog/product")->getIdBySku($data['bundled_sku']);
if (!$new_bundled_item_id)
    throw new Exception('Product with sku '. $data['bundled_sku'] .' does not exists');

// Load existing bundled product
$productCheck = Mage::getModel('catalog/product')->load($bundled_product_id);

// Set raw option data
$bundleOptions = array();
$bundleOptions = array(
    0 => array(
        'title' => $data['bundled_title'],
        'default_title' => $data['bundled_title'],
        'option_id' => '',
        'delete' => '',
        'type' => 'select',
        'required' => '1',
        'position' => '1'
    )
);

// Load bundle item ids
$bundled_item_ids = array();
$selectionCollection = $productCheck->getTypeInstance(true)->getSelectionsCollection(
    $productCheck->getTypeInstance(true)->getOptionsIds($productCheck), $productCheck
);
foreach($selectionCollection as $option)
    $bundled_item_ids[] = (int)$option->product_id;
foreach ($bundled_item_ids as $bundled_item_id)
    if ($new_bundled_item_id !== $bundled_item_id)
        $bundled_item_ids[] = $new_bundled_item_id;

// Set raw selection data
$bundleSelections = array();
foreach ($bundleOptions as $option_id => $bundleOption) {
    foreach ($bundled_item_ids as $selection_id => $bundled_item_id) {
        $bundleSelections[$option_id][$selection_id] = array(
            'product_id' => $bundled_item_id,
            'delete' => '',
            'selection_price_value' => 0.00,
            'selection_price_type' => 0,
            'selection_qty' => 1,
            'selection_can_change_qty' => 0,
            'position' => 0,
            'is_default' => 1
        );
    }
}

// Set flags
$productCheck->setCanSaveCustomOptions(true);
$productCheck->setCanSaveBundleSelections(true);
$productCheck->setAffectBundleProductSelections(true);

// Register flag
Mage::register('product', $productCheck);

// Set option & selection data
$productCheck->setBundleOptionsData($bundleOptions);
$productCheck->setBundleSelectionsData($bundleSelections);

// Save changes
$productCheck->save();