Welcome to the STD forum.
Your doctor is exactly right. The large majority of people with very low HSV-2 test values, like yours, are not infected. Repeat testing in a few weeks is exactly the right thing to do. If that result is clearly negative (i.e., a value 0.9 or less) you can be positive you don't have it. If it remains in the equivocal range -- any result from 0.9 to 3.5 -- then a confirmatory blood test is required to sort it out, such as the HSV Western blot test.
The details of the HSV-2 blood tests and how they were are covered in this thread; take a look at it.
http://www.medhelp.org/posts/show/593272
To the specific questions:
1) See above, and the link.
2) There is no known cause for equivocal or falsely elevated test results. It appears to be random.
3) Your "UTI" probably has nothing to do with it -- but see my comments below.
4,6) Actual herpes blisters/sores may itch, but otherwise herpes doesn't cause genital area itching. HSV also doesn't cause genital rash except for blisters/sores.
5) Conceivably you have a new infection, in which case repeat testing will show a more strongly positive result. This is one of the reasons to have a repeat test in a few weeks.
7) There is no set period for repeat testing. Six weeks is probably about right.
Going back to your "UTI": Urinary tract infections are rare in healthy young (under age 40) men. Many physicians not up to speed on STDs diagnose UTI when the actual problem is nongonococcal urethritis (NGU), which is an STD. There are mixed messages about your own provider in this instance: doxycycline is the standard treatment for NGU, but usally not for UTI. So I'm not certain exactly what your doctor thought you had. On the other hand, the main symptoms of NGU are discharge of pus or mucus from the penis, sometimes with slightly uncomfortable urination but usually not overt pain.
Could that problem have been the initial symptoms of genital herpes? Possibly yes. But most herpes inside the urethra is very painful; one patient of mine said it was the worst pain he ever had. And most herpetic urethritis also has typical penile herpes blisters/sores. The probability of either herpes or NGU depends somewhat on your sexual exposures. For example, any recent unprotected sex with new partners?
At this point, you should discuss these thoughts with your doctor. Let me know what he says. But most likely you don't have herpes.
Good luck-- HHH, MD