Welcome to the Q&A Forum

If you only want your indexed pages, you can add the SeoQuake plugin to your browser than do a google search like site:http://www.yoursite.com/  . Be sure to chose "show with omitted results included". This search will show all the indexed pages of your site. From Google settings, chose 50 or 100 results per page and than, above the results, SeoQuake has an option to download as CSV.

Assuming that you don't have thousands of pages, save them from each Google results page and get them together in one file. Than, you can sort them out and do whatever you want to. Good luck!

Our website offers an affiliate program and every affiliate gets a link http://www.ourwebsite.com/?affiliateID.

Because we get many such links we use redirects to avoid duplicate content. Unfortunately we have 302 redirects set up and I want to make them 301. Many of our affiliates build backlinks using their http://www.ourwebsite.com/?affiliateID as the URL. If such links were redirected through a 301, would they pass any juice? Can our site get penalized by search engines for having backlinks to URLs that contain affiliate IDs, URLs that are 301 redirected to our homepage lets say?

If you only want your indexed pages, you can add the SeoQuake plugin to your browser than do a google search like site:http://www.yoursite.com/  . Be sure to chose "show with omitted results included". This search will show all the indexed pages of your site. From Google settings, chose 50 or 100 results per page and than, above the results, SeoQuake has an option to download as CSV.

Assuming that you don't have thousands of pages, save them from each Google results page and get them together in one file. Than, you can sort them out and do whatever you want to. Good luck!