Search for that term in the DBI manual, read carefully to understand all the ways they can make your code better, and work it into your code. Basically, you create a query string with one or more question mark characters where a value would be -- each question mark is a "placeholder" for a value. Then you do $sth=$dbh->prepare($statement) in the normal way, and when you execute it, you pass values for each placeholder: $sth->execute(@values) (or $sth->execute($val1,$val2,...)), as shown in the code I posted above.

I was considering the Load Data Local Infile things, but realized my limitation when I needed to compare stuff before the Inserting/Updating happens.

I'm not understanding what your "limitation" is. You just open an output file before the loop; within the loop, instead of executing an insert statement, you print a line to the file; after the loop you close the file and execute a "LOAD DATA LOCAL INFILE ..." statement. You can't use this approach for the updates -- those still need to be executed on each loop iteration.

(updated to improve grammar)