I have had this same problem. Too much ejactulation damages the urethral tract causing the release of an inflammatory hormone called prostaglandin E-2 (PGE-2) which causes further irritation. Because PGE-2 is found in semen, if your semen has high levels of PGE-2, it will create a mini "snowball-effect" and be very painful.
First you need to stop ejaculating. This may sound like a chore but just think about the fact that you are tearing a hole in your urethra outside the seminal duct.
Then you need to take fish oil (esp. Omega 3 and 6; GLA) with every meal and supplement 5-HTP and GABA and a multi vitamin. Make sure you get non-synthetic 5-HTP; a natural extract (a common source is griffonia simplicifolia seed).