It is possible that two of the diagnoses that you were offered were accurate. The initial diagnosis of kidney infection can be expanded a little to include kidney stones as well. And the diagnosis regarding the prostate problem can also be accurate as both these conditions can coexist.
A kidney stone can cause obstruction to urine outflow and this obstruction may be partial or complete. Due to pooling of urine in the kidney or reflux of urine (if the stone is somewhere in the ureter), there can be a resultant infection of the kidney and kidney damage as well. An Xray of the abdomen and pelvis will help detect the presence of any stone in the urinary tract.
Prostate inflammation resulting in enlarged prostate (as determined on the digital rectal exam) can be due to a bacterial infection or may be due to noninfective causes. The source of the inflammation can be ascertained on urinalysis or a semen examination for infective organisms.
Both kidney and prostate-related problems can go through phases of exacerbation and remissions.
You will need to take care to avoid aggravating factors such as caffeine, alcohol, citrus fruits and juices, spicy foods, etc. You will also need to avoid sitting for prolonged periods or on inadequately padded surfaces. Avoid putting excessive pressure on the perineal region as this can cause further irritation to the prostate gland.
You will need to go on a course of antibiotics for the infection of the prostate gland and the duration of treatment can be about 15-21 days or even longer. Increase your fluid intake to over 2000 ml per day and increase consumption of natural sources of calcium.
Application of heat to the back and sitting in a hot bath for 10-15min can also provide significant pain relief.
Do post your urinalysis results in a post here so that we can provide a more accurate diagnosis.