Martha Christie ("Your Own Perfect Medicine") cured her candida doing UT. Urine has anti-microbial properties so I would have thought it was fine to use during any infection but I also read that if you do have a bladder or kidney infection, you should use caution (maybe use it homeopathically).
Having said that I remember Andreas (Moritz) saying on his forum that his mother cured a kidney infection with urine (don't know whether she was drinking it or doing rubs).
Yes I believe if you are taking any kind of drug it's best not to ingest urine or you will just recycle the metabolites.
I don't sweat very much so don't have that particular problem but I've had a kind of similar experience when I went swimming 2 days after I did a 20 mins full body urine rub (the urine had aged and was quite smelly). When swimming I could smell the urine coming off me in the water (even though it was done 2 days previous). Luckily there weren't many people at the pool! I think maybe if it's big problem just use fresh morning urine rather than aged then shower afterwards. You will still get benefits. Also make sure your diet is clean as the smell should be fairly inocuous then.