Doubleaaaron has given a good round up of possibilities. Other things to note are:
Small amounts of microscopic blood (only seen via testing) within the urine (hematuria), suggests injury to the upper urinary tract (kidneys), whilst observable blood (with the eyes) suggests injury to the lower tract (i.e. bladder or urethra). However this is not always the situation.
I would also recommend checking out the following website, especially when an infection has been ruled out: http://www.wrongdiagnosis.com/symptoms/blood_in_urine/causes.htm
& http://www.wrongdiagnosis.com/p/proteinuria/causes.htm
The trick however is to not read too much, because "Doctor" Google can get it wrong sometimes. Leave it up the professionals to test you properly.
I wish you well.
A shadow could be many things including a cyst. A ct scan can help with that. I had one. Which through a ct scan was determined to just be a cyst. But there are other things it can be as well. Severe scarring or cancer is among other things. Not saying you have that just saying that is some of the things it could be. Any kind of protein in the urine is not normal especially consistently. Blood can be from the bladder it doesn't necessarily come from the kidney.
i also have blood in my urine at all times. not sure why have had all test ran and nothing wrong, my dr says sometimes its just like that. i have lots more when i have utis. dont stress it to much with what test you already had am sure your going be fine.