Mkew,.
Congratulations on educating yourself about living kidney donation. you are correct to be concerned about future health complications. There hasn't been much in long term follow up of kidney donors. Most research is retrospective and some data may be missing about complications years out related to donors.
You may want to seek a second opinion from a good nephrologist to evaluate you independent of the transplant hospital. Get copies of all your labs and testing. You can also discuss this with your primary care doctor. If you are concerned about hormonal issues speak with your gyn and or an endocrinologist and get their input into how safe this elective surgery will be for you. If you were having any other type of surgery you would most likely seek a second opinion, how much more so this is needed when the surgery does not benefit you physically and may put you at risk.
In terms of the cystoscopy, I've never had one but you can look online for information. My husband had one many years ago and he said it wasn't pleasant but they do sedate you and you have little recollection or discomfort. I imagine similar to a colonoscopy with sedation. Here is a link
http://kidney.niddk.nih.gov/kudiseases/pubs/cystoscopy/Most important make sure your kidney function is good enough to tolerate and compensate for losing 50% of your nephrons (the cells that filter in the kidney). Each center has their own criteria and unfortunately there are no federal guidelines that are enforced among all transplant centers. Make sure you know what your numbers related to kidney function and discuss this with a competent kidney specialist who has your interests in mind.
In terms of which kidney is removed. Most often the left is removed because of a longer renal vein which is beneficial to the recipient during the transplant. If the donor has one kidney that has a cyst or difficult vasculature, or one has higher function than the other (they are not always 50/50 and there are tests for that as well) then the donor always keeps the kidney with better function or quality. So sometimes they may take the right one.
Keep in mind any financial issues, health insurance, time off from work, recuperation, family support and all the other psychosocial issues that come into play.
Glad to hear you are thinking about this carefully. Keep researching and learning and feel free to share what you find.
Best of luck,
Sherri