All credit goes to Brandon. I searched and found this thread last night which was ultimately the solution. I'll post the script below as that thread was a little confusing to follow until they got it working.
You'll need to convert all MH File fields to a Matrix field first. Then run the script below.
Make sure to replace XX with your Matrix field ID, YY with your File
column ID, and ZZ with your file upload directory ID.
<?php
// Converts Mark Huot's File Field with multiple images to a Matrix column
mysql_connect("localhost", "db_username", "db_password") or die(mysql_error());
mysql_select_db("database_name") or die(mysql_error());
$query = mysql_query('SELECT site_id, entry_id, field_id_XX FROM exp_channel_data WHERE field_id_XX IS NOT NULL');
while ($row = mysql_fetch_assoc($query)) {
// get the file names
$files = array_filter(preg_split('/[\r\n]/', $row['field_id_XX']));
// add them to exp_matrix_data
foreach ($files as $i => $file) {
mysql_query('INSERT INTO exp_matrix_data (site_id, entry_id, field_id, row_order, col_id_YY)
VALUES ('.$row['site_id'].', '.$row['entry_id'].', XX, '.$i.', "{filedir_ZZ}'.$file.'")');
}
}
?>