Kidney stones that can be as small as a grain of sand can be extremely painful when they move and when you pee when they come out.
Catch your urine in a clean glass and look at it. Kidney stones can be very fine line sand. If your urine is cloudy, red (as long as you have not eaten strongly coloured food like beetroot), dark, this could mean an infection.
Did the urine specimen get checked out by the laboratory? Dip stick urine tests sometimes do not show up any problem, but the laboratory can pick it up.
It may be painful to pee if you have skin soreness due to the std, or a fungal infection.
If all the tests come back normal, get the doctor to do a swab to send to the laboratory to check for any bacterial or fungal problems.
In the meantime, do NOT use normal soap, bath or shower gels. These dry the skin and can cause irritation to the skin. Just use plain water.
It is possible that you may have an allergic reaction to some of the lubes that you have used and it is also possible that you may have a latex allergy if you use condoms. Use the latex free ones.
Use non biological washing detergents and fabric softeners that are suitable for people with allergies. Only wear cotton underpants and put a clean pair on every day and make sure you keep clean. Wash your hands every time after you use the toilet and wash your hands before touching your penis.
As a home help remedy, after washing and gently drying your penis, apply natural set yogurt to the skin area. If there is a skin soreness due to fungal problems, this will help to ease the discomfort.
You can also purchase from the pharmacy without a prescription, emollients that can be used instead of soap.