Hopefully one of the guys will chime in here, but my guess is that the pain you experienced may have been due to your having an enlarged prostate, which narrows the urethra and makes it difficult to maneuver the cystoscope through that area. Although I'm not a guy, I used to have a moderate amount of pain during cystoscopies, but the urologist discovered that things went better for me if he tipped the table slightly (with my head lower than my feet). I also used to get a lot of bladder spasms for several hours after a cystoscopy, but that has definitely improved with time. You might ask your urologist to prescribe an antispasmodic, such as Vesicare, to take beforehand and maybe afterwoard if you have pain or spasms.
In terms of later treatments you mention, if it's BCG instillations that is done with a very narrow catheter, so I've found that to be way easier than the cystoscope.
I think men have it harder due to the longer urethra and the likelihood of having prostatic enlargement!
Ann
Small TA Grade 1, May-06; recur (2 tiny), same, June-08; TURBTs both times. BCG begun July-08, dosage to 1/3rd May-10, completed treatment December-11. All clear since 2008.