$headers = array ('0' => 'id', '1' => 'Name', '2' => 'Balance', '3' => 'Date', '4'=> 'Region', '5' => 'Segment', '6' => 'Manager', '7' => 'Contract');

$content = array (
array ('0' => 'id1', '1' => 'Name1', '2' => 'balance1', '3' => 'date1', '4'=> 'region1', '5' > 'segment1', '6' => 'manager1', '7' => 'сontract1'),
array ('0' => 'id2', '1' => 'Name2', '2' => 'balance2', '3' => 'date2', '4'=> 'region2', '5' > 'segment2', '6' => 'manager2', '7' => 'сontract2'),
array ('0' => 'id3', '1' => 'Name3', '2' => 'balance3', '3' => 'date1', '4'=> 'region3', '5' > 'segment3', '6' => 'manager3', '7' => 'сontract3'),
array ('0' => 'id4', '1' => 'Name4', '2' => 'balance4', '3' => 'date4', '4'=> 'region4', '5' > 'segment4', '6' => 'manager4', '7' => 'сontract4'));

$data = array (
'id' => array ('0' => 'id1', '1' => 'id2', '2' => 'id3', '3' => 'id4'),
'Name' => array ('0' => 'name1', '1' => ''name2', '2' => ''name3', '3' => ''name4'),
'Balance' => array ('0' => 'balance1', '1' => 'balance2', '2' => 'balance3', '3' => 'balance4'),
'Date' => array ('0' => 'date1', '1' => 'date2', '2' => 'date3', '3' => 'date4'),
 'Region' => array ('0' => 'region1', '1' => 'region2', '2' => 'region3', '3' => 'region4'),
 'Segment' => array ('0' => 'segment1', '1' => 'segment2', '2' => 'segment3', '3' => 'segment4'),
'Manager' => array ('0' => 'manager1', '1' => 'manager2', '2' => 'manager3', '3' => 'manager4'),
'Contract' => array ('0' => 'contract1', '1' => 'contract2', '2' => 'contract3', '3' => 'contract4'));

$content = array (
array(
'A{+order=S.MMStatus&how=ASC}...{width:12px}|printClientStatus2' => '3',
'Название{+order=S.Name&how=ASC}...hatch|printClientName' => 'testClient1',
'Баланс...mask|printNumber' => '150.0000',
'Дата последней рассылки...mask|printClientType' => '',
'Регион{crmclients&order=S.CRMRegionsID&how=ASC}...mask|cRegions' => '',
'Сегмент{+order=S.CRMMarcetSegmentID&how=ASC}...{width:20px}' => '',
'Менеджер{+order=S.ManagerID&how=ASC}...mask|printUser' => '2296',
'Договор|cClientRevision' => '2'),

array(
'A{+order=S.MMStatus&how=ASC}...{width:12px}|printClientStatus2' => '3',
'Название{+order=S.Name&how=ASC}...hatch|printClientName' => 'testClient2',
'Баланс...mask|printNumber' => '397.0000',
'Дата последней рассылки...mask|printClientType' => '',
'Регион{crmclients&order=S.CRMRegionsID&how=ASC}...mask|cRegions' => '',
'Сегмент{+order=S.CRMMarcetSegmentID&how=ASC}...{width:20px}' => '',
'Менеджер{+order=S.ManagerID&how=ASC}...mask|printUser' => '2296',
'Договор|cClientRevision' => '2'));

$data = array();
foreach ($content as $line) {
    foreach ($line as $key => $val) {
        $data[$headers[$key]][] = $val;
    }
}

$headers = [
    '0' => 'id',
    '1' => 'Name',
    '2' => 'Balance',
    '3' => 'Date',
    '4' => 'Region',
    '5' => 'Segment',
    '6' => 'Manager',
    '7' => 'Contract'
  ];

$content = [
  [
    '0' => 'id1',
    '1' => 'Name1',
    '2' => 'balance1',
    '3' => 'date1',
    '4' => 'region1',
    '5' => 'segment1',
    '6' => 'manager1',
    '7' => 'сontract1'
  ],
  [
    '0' => 'id2',
    '1' => 'Name2',
    '2' => 'balance2',
    '3' => 'date2',
    '4' => 'region2',
    '5' > 'segment2',
    '6' => 'manager2',
    '7' => 'сontract2'
  ],
];

$data = array();
foreach ($headers as $key => $line) {
    $data[$line] = array_column($content, $key);
}

echo '<pre>';
print_r($data);

Array
(
    [id] => Array
        (
            [0] => id1
            [1] => id2
        )

    [Name] => Array
        (
            [0] => Name1
            [1] => Name2
        )

    [Balance] => Array
        (
            [0] => balance1
            [1] => balance2
        )

    [Date] => Array
        (
            [0] => date1
            [1] => date2
        )

    [Region] => Array
        (
            [0] => region1
            [1] => region2
        )

    [Segment] => Array
        (
            [0] => segment1
            [1] =>
        )

    [Manager] => Array
        (
            [0] => manager1
            [1] => manager2
        )

    [Contract] => Array
        (
            [0] => сontract1
            [1] => сontract2
        )

)