Download the Java JRE if it's not already installed https://java.com/en/download/
Download ebird-flickr-downloader.jar (under RELEASES tab)
Open a command prompt
Switch to the directory that has ebird-flickr-downloader.jar
Argument 1 to the program is the directory of your "MyEBirdData.csv" file from https://ebird.org/downloadMyData
Argument 2 is your flickr username (so that photos from shared checklists aren't also downloaded)
Run the program using java -jar jarfilename arg1 arg2

EXAMPLE, if ebird-flickr-downloader.jar is in downloads directory and "MyEBirdData.csv" file is in documents/ebird/mydata
cd downloads
java -jar ebird-flickr-downloader.jar documents/ebird/mydata flickrusername

NOTE: I haven't figured out a way to download originals from flickr. The API says original download is only available for PRO users. However it seems to return the largest possible size below that.  If you have a lot of photos you may want to consider signing up for PRO, at least temporarily.