Hello - during a recent purge of the remains of the Affiliate system from an installation of a 6.4 Pro version, I made a list of the changes. (Maybe someone could script these, but they're fairly easy to do.)

BACKUP your Store and Database first!!!

FILES TO DELETE (64)
/popup_affiliate_help.php
/admin/includes/languages/affiliate_english.php
/admin/includes/languages/english/affiliate_password_forgotten.php
/admin/includes/languages/english/affiliate_affiliate.php
/admin/includes/languages/english/affiliate_affiliates.php
/admin/includes/languages/english/affiliate_banner_statistics.php
/admin/includes/languages/english/affiliate_banners_banners.php
/admin/includes/languages/english/affiliate_banners_build_cat.php
/admin/includes/languages/english/affiliate_banners_build.php
/admin/includes/languages/english/affiliate_banners_category.php
/admin/includes/languages/english/affiliate_banners_product.php
/admin/includes/languages/english/affiliate_banners_text.php
/admin/includes/languages/english/affiliate_banners.php
/admin/includes/languages/english/affiliate_central.php
/admin/includes/languages/english/affiliate_clicks.php
/admin/includes/languages/english/affiliate_contact.php
/admin/includes/languages/english/affiliate_details_ok.php
/admin/includes/languages/english/affiliate_details.php
/admin/includes/languages/english/affiliate_faq.php
/admin/includes/languages/english/affiliate_info.php
/admin/includes/languages/english/affiliate_invoice.php
/admin/includes/languages/english/affiliate_logout.php
/admin/includes/languages/english/affiliate_news.php
/admin/includes/languages/english/affiliate_newsletter.php
/admin/includes/languages/english/affiliate_password.php
/admin/includes/languages/english/affiliate_payment.php
/admin/includes/languages/english/affiliate_reports.php
/admin/includes/languages/english/affiliate_sales.php
/admin/includes/languages/english/affiliate_signup_ok.php
/admin/includes/languages/english/affiliate_signup.php
/admin/includes/languages/english/affiliate_statistics.php
/admin/includes/languages/english/affiliate_summary.php
/admin/includes/languages/english/affiliate_terms.php
/admin/includes/languages/english/modules/newsletters/affiliate_newsletter.php
/admin/includes/languages/english/popup_affiliate_help.php

/includes/languages/affiliate_english.php
/includes/languages/english/affiliate _payment.php
/includes/languages/english/affiliate_affiliate.php
/includes/languages/english/affiliate_banners_banners.php
/includes/languages/english/affiliate_banners_build_cat.php
/includes/languages/english/affiliate_banners_build.php
/includes/languages/english/affiliate_banners_category.php
/includes/languages/english/affiliate_banners_product.php
/includes/languages/english/affiliate_banners_text.php
/includes/languages/english/affiliate_banners.php
/includes/languages/english/affiliate_central.php
/includes/languages/english/affiliate_clicks.php
/includes/languages/english/affiliate_contact.php
/includes/languages/english/affiliate_details_ok.php
/includes/languages/english/affiliate_details.php
/includes/languages/english/affiliate_fag.php
/includes/languages/english/affiliate_info.php
/includes/languages/english/affiliate_logout.php
/includes/languages/english/affiliate_news.php
/includes/languages/english/affiliate_newsletter.php
/includes/languages/english/affiliate_password_forgotten.php
/includes/languages/english/affiliate_password.php
/includes/languages/english/affiliate_reports.php
/includes/languages/english/affiliate_sales.php
/includes/languages/english/affiliate_signup_ok.php
/includes/languages/english/affiliate_signup.php
/includes/languages/english/affiliate_summary.php
/includes/languages/english/affiliate_terms.php
/includes/languages/english/popup_affiliate_help.php

DATABASE TABLES TO DROP (11)
affiliate_affiliate
affiliate_banners
affiliate_banners_history
affiliate_clickthroughs
affiliate_news
affiliate_newsletters
affiliate_news_contents
affiliate_payment
affiliate_payment_status
affiliate_payment_status_history
affiliate_sales

FILES TO EDIT (15)
/admin/edit_textdata.php - del line 489
/admin/newsletters.php - del lines 232-233; 283-284; 342-343; 389-390
/admin/includes/languages/english.php - del lines 238

/admin/header_navigation2.php - change line 26 to read:
$box_files_list02 = array( array('taxes', 'taxes.php' , BOX_HEADING_LOCATION_AND_TAXES),

/admin/includes/languages/english/configuration.php - del lines 45-46
/admin/includes/languages/english/index.php - del lines 79-84
/admin/includes/languages/english/newsletters.php - del line 59

/checkout_process.php - del lines 358-361

/includes/application_top_cre_setting.php - del lines 19-26
/includes/filenames.php - del lines 258-291
/includes/languages/english.php - del lines 504-515;
/includes/runtime/global/GA_global_footer.php - del lines 26; 58

/templates/content/product_info_tabs.tpl.php - del lines 156-158
/templates/content/product_info.tpl.php - del lines 145-147
/templates/default/modules/product_discription.php - del lines 27-31

DATABASE EDITS (17) (easiest to use phpmyadmin and Search on %affil%)
EDIT DATABASE TABLE infobox_configuration (1)
delete affiliates.php (under infobox_file_name)

EDIT DATABASE TABLE admin_files
delete all of the following under admin_file_names (16):
affiliate.php
affiliate_affiliates.php
affiliate_clicks.php
affiliate_banners.php
affiliate_contact.php
affiliate_invoice.php
affiliate_payment.php
affiliate_popup_image.php
affiliate_sales.php
affiliate_statistics.php
affiliate_summary.php
affiliate_news.php
affiliate_newsletters.php
affiliate_validcats.php
affiliate_validproducts.php
popup_affiliate_help.php

EDIT DATABASE TABLE infoxbox_heading
delete under box_heading (5):
affiliate_info x 5

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As you can see, the Cre coders left quite a bit behind.
Hope this helps!
Simon