I recommend that you see a urologist, or your primary care provider for formal evaluation. There are multiple causes for abnormal discoloration of semen, some of which may be benign and others more severe. One of the more common causes is the presence of decomposing blood in the semen. This is due to bleeding into the genital tract, which can occur anywhere from the testicles and seminal vesicles, along the vas deferens which is the tract connecting the testicles to the urinary tract. Bleeding from the prostate and urethra are also possible. Based on your text, pain in the penis with manipulation may suggest traumatic injury to the urethral lining. This may be due to injury or repetitive irritation, as with excessive masturbation. Cessation from potentially traumatic activities such as masturbation and sexual activity until the pain and discoloration resolves may be of help. Again, please speak with your urologist.