Yes, the PDF Stamper does stamp the file when used with Manual checkout if you have checked the "Send Product Download Links in the Email" option for manual checkout. If you read the help text for each of the settings field in the manual checkout it will give you an idea of what it does.
Making the coupon field required for manual checkout will need to be custom coded. You can contact us here for custom development discussion:
http://support.tipsandtricks-hq.com/contact