WAMP data compare script taking very long - php

Question

I'm running a comparison of some data using PHP to access MySQL tables. The script takes well over an hour to run. We're dealing with about 100k rows in the source data and 300k in each of the target tables, i.e. two tables.
There's no more than 10 columns total in each table.
Here is the script:
$query = "SELECT bbva_check_deductions.empno, bbva_check_deductions.idr, bbva_check_deductions.current1, bbva_job.paygroup
FROM bbva_check_deductions
LEFT JOIN bbva_job
ON bbva_check_deductions.empno = bbva_job.file_nbr
ORDER BY current1 DESC, EmpNo DESC, IDR DESC";
$result_set = mysql_query($query,$connection);
while ($result = mysql_fetch_assoc($result_set)) {
$emplid = compare_filter($result['empno']);
$oldCode = compare_filter($result['idr']);
$origCode = $oldCode;
$payGroup = compare_filter($result['paygroup']);
$codes = array('DC6', 'HTH', 'DM4', '4UP', 'DC1', 'DC3', 'DC4', 'DEN', 'DCR', 'MDR', 'PRK', 'VIS', '41K');
//CALCULATE WEEK NO
if ($payGroup == "J2C") {$week = 24;}
elseif ($payGroup == "J2E") {$week = 26;}
else {$week = 22;}
//QUERY TRANSLATION TABLE FOR TRANSLATED VALUE
$translate_query = "SELECT * FROM translation WHERE sourceValue = '{$oldCode}'
AND sourceField LIKE '%ded_code%' LIMIT 1";
$translate_result_set = mysql_query($translate_query, $connection);
if (mysql_num_rows($translate_result_set) > 0) {
$translate_result = mysql_fetch_assoc($translate_result_set);
$oldCode = compare_filter($translate_result['translatedValue']);
}
//DETERMINE IF MEMO
if ($oldCode == "GTL" || $oldCode == "BLI" || $oldCode == "BLT" || $oldCode == "HIC" || $oldCode == "DM4") {
$queryField = "memo_code"; $queryTable = "pf_check_memo";
} else {
$queryField = "deduction_code"; $queryTable = "pf_check_deductions";
}
$compare_query = "SELECT {$queryField}, amount_field_for_payroll
FROM {$queryTable}
WHERE empl_id = {$emplid}
AND {$queryField} LIKE '%{$oldCode}%'
AND week_number = {$week}
LIMIT 1";
$compare_result_set = mysql_query($compare_query, $connection);
if (mysql_num_rows($compare_result_set) != 0) {
$compare_result = mysql_fetch_assoc($compare_result_set);
//PREP COMPARE FIELDS
$amount = compare_filter($result['current1']);
$compare_amount = compare_filter($compare_result['amount_field_for_payroll']);
$negCodes = array('DC6', 'HTH', 'DM4', '4UP', 'DC1', 'DC3', 'DC4', 'DEN', 'DCR', 'MDR', 'PRK', 'VIS', '41K');
if (in_array($oldCode,$negCodes)) {$compare_amount = $compare_amount * -1;}
//AMOUNT COMPARE
direct_compare_basic($amount,$compare_amount,"amount","bbva_check_deductions","Y",$origCode,$oldCode);
} else {$content .= $emplid . $separator . "" . $separator . "Emplid + Deduction Code + Pay Group" . $separator . 'bbva_check_deductions' .
$separator . field_prep($emplid . " - " . $oldCode . " - " . $payGroup) . $separator . "No Record Found in PF for week {$week}" . $separator . "Y" . $separator . "Y" .
$separator . $origCode . $separator . $oldCode . $break;}
Then it just writes to a .CSV file.
My functions do not call any additional queries, just formatting stuff. I'm running InnoDB tables and have indexes for all columns being used. My PC is running WAMP, it's got 16G of RAM and a quad core processor. The HDD is 7200 RPM.
Seems like it is taking far too long to me. Any ideas?