Ended up finding the issue:
1)First FTP on the fly does not work very well, for some reason password was not accepted with on the fly
2)Bucket-acl-private is incorrect even though I had specific permissions to edit the bucket

    S3_REMOTE=":s3,provider=AWS,access_key_id=$ACCESS_KEY,secret_access_key=$SECRET_KEY:$BUCKET"
    RCLONE_FLAGS="--s3-chunk-size 100M --s3-upload-cutoff 200M --retries 5 --low-level-retries 10 --progress --checksum"

    # Create a temporary named FTP remote
    rclone config create "$FTP_REMOTE_NAME" ftp host="$FTP_HOST" user="$FTP_USER" pass="$FTP_PASS" --obscure

#create a temporary directory to check the md5
    TEMP_DIR="./temp_md5"
    mkdir -p "$TEMP_DIR"

    if [ -z "$FTP_FOLDER" ]; then
        rclone copy "$FTP_REMOTE_NAME:md5.txt" "$TEMP_DIR" --quiet
        rclone copy "$FTP_REMOTE_NAME:$FTP_FILE" "$TEMP_DIR" --quiet