With all your testing, did they ever mention white blood cells in your urine? Did you test for a urinary tract infection?
You had protected oral sex, and though I'm not sure what you mean by "loose", it's hard to believe that her saliva would go all the way down your penis and into your urethra, which is what would have had to happen to cause any kind of infection.
Beyond that, saliva isn't the biggest concern with oral sex. Gonorrhea and chlamydia reside in the throat, so with oral sex, especially when given to a penis, the concern is if the penis is exposed to the throat. Since you wore a condom, that didn't happen.
It's not uncommon for urine to be more yellow in the morning - you haven't urinated in several hours, or had anything to drink, so it's more concentrated. Yellow is an okay color for urine.
No STD causes swelling of the penis. That happens with trauma to the penis, like injuries, usually.
It's normal to have a small amount of clear discharge, as well. You've probably always had this, but didn't pay any attention since you didn't have cause to be anxious.
Frequency and urgency to urinate are signs of a urinary tract infection. This is why I asked if they tested you for that, or just did STD testing. It can also happen if you are drinking a lot of caffeine and/or alcohol, and not enough water. Some people get it when you drink too many sports drinks or energy drinks. If you drink a lot of any of those, cut way back and increase the water.
Your sore throat, stomach discomfort and chills aren't related to any STD.
Ureaplasma is commonly found in the body. Whether it needs to be treated or not depends on the levels found.
1. Some of STIs like Syphillis have a longer incubation period. Can you suggest if I should get tested again for any STIs, any other infection or it could be related to something else like prostatis?
Syphilis and herpes produce sores. If you don't get any, I wouldn't bother testing again. Your symptoms don't indicate either of those.
2. Also, the STI tests done were using urine and blood. Are penile swabs tests better for diagnosing STIs? I'll appreciate any other suggestions.
Your tests were fine. The tests done by urine are just as accurate as swab tests.