Brief Answer:
UTI possible, Renal stone or an STD

Detailed Answer:
Thank you for asking

As far as the symptoms of burning micturition and pain in flanks are concerned, Two things need to be ruled out. A urinary tract infection or a calculus / stone.

If you have been coitally active and had unprotected coitus recently, STD evaluation will also be required.

The good start will be a simple urine routine exam and an abdominal sonogram to see if any calculus or sludge is there in the tract causing the symptoms.

It is said that drinking plenty of water is the best way to get rid of the organisms and clearing the pathway of them. SO drink as much fluid as you can, At least 12 to 16 glasses of water a day.
Then comes the role of hygiene, Front to back unidirectional wiping , using hot saline baths, sits baths, Avoiding unnecessary douchings, Not using Beauty soaps or perfumes down there, Good toilet hygiene, Post coital voiding immediately, avoiding unnecessary manual or digital or lingual manipulation of the area to avoid troubles.
Recently Use of Cranberry juices 10-12 ounces daily work like charm. These juices have proanthracyclins in them which doest allow organisms to stick to the pathway epithelium and thus decrease the predispositions to infections.
Those who have trouble with pain during micturition can get relief from bladder analgesic like Phenazopyridine if Sulfa allergies are not the problem.
Recent use of Intra bladder Instillations of Hyaluronic acids and chondroitin sulfates have proved very efficient.
Rest the antibiotics like quinolones, cephalosporins an. penicillin, sulfonamides and aminoglycosides with other symptomatic treatment is advised after being prescribed. Symptomatic treatment is used like antispasmodics like phloroglucinols or hyoscine etc and simple analgesics like acetaminophen etc suffice.

Nutshell, Drink plenty of fluids, cranberry juices 10- 12 ounces a day, an antibiotic will be required after work up and antispasmodics like phloroglucinols will help the pain.

Now the color of the urine or the black specks you mentioned, They may be some medicines effects like metronidazole,nitrofurantoin, cascara or senna laxatives, methocarbamol, sorbitol, and the phenol derivative cresol a common disinfectant ingested by alcoholics, or they may be because of some iron supplements or diet rich in iron you recently took.

But if the black color of urine comes up persistently then it will need some work up to sort out some grievous troubles.

Spots on the penis if dont bother than all clear. usually they are innocuous and self resolve. Godo toilet and coital hygiene and loose garments will help the penis.

Your condition is not difficult and you are a young healthy man. You should be fine.

I hope it helps. Take good care of yourself and dont forget to close the discussion please.

May the odds be ever in your favour.

Regards
Khan

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