Resolved by (assuming saved in extensions folder with path below).
LocalSettings.php:
require_once($IP.'/extensions/MagicNumberedHeadings/MagicNumberedHeadings.php');
Modify parsing order by editing the extension above (ie MagicNumberedHeadings.php):
replace line 49
$wgHooks['ParserBeforeInternalParse'][] = 'MagicNumberedHeadingsParserBeforeInternalParse';
with
$wgHooks['InternalParseBeforeLinks'][] = 'MagicNumberedHeadingsInternalParseBeforeLinks';
And line 62
function MagicNumberedHeadingsParserBeforeInternalParse( &$parser, &$text, &$strip_state ) {
with
function MagicNumberedHeadingsInternalParseBeforeLinks(&$parser, &$text, &$stripState) {
Finally, update get method by changing line 63
MagicWord::get
to
$parser->getMagicWordFactory()->get