I use sevin 5% garden dust on all my chickens. I usually dust the entire chicken but the highest concentration of mites are usually found in the vent area, tail area, and thighs, dust those well. If you prefer not to dust, you can bathe him using a dog/puppy flea and tick shampoo. Just make...
Sounds as if your rooster has a very bad mite infestation and what you may be seeing on the base of the tail are eggs from the mites. Check his back end very carefully in the daytime, if you see no bugs running around (they are very quick, look hard) check at night also as some mites only feed...