I'm getting my first colonoscopy: What's your advice?

I always knew this day would come, since my mom has ulcerative colitis and my dad has celiac disease and diverticulosis, but I'd always assumed it wouldn't come quite this soon...I have my first colonoscopy scheduled on Thursday. Watching my mom suffer through the prep every year, I know it's going to be unpleasant, but I need to make sure it's WORTHWHILE. Unfortunately, I don't have much confidence in the gastroenterologist/practice who will be doing the procedure -- he did an upper endoscopy a month ago that I have some concerns with his findings/methods.*

I've been chronically and inexplicably ill since June with extreme fatigue, low-grade fever (99-100), nausea and urinary frequency; more recently (after the endoscopy, in fact, although I don't think there's a causative relationship there other than they tell you to pay attention to your stool afterwards, which is something I never really did previously), I have had some issues with my anal area feeling "moist" (occasionally area will be wet in underwear) and like there's something moving down there, and I've seen increasing amounts of mucous and occasionally blood spots in my stool. With the as-of-yet unexplained fever of unknown origin and slightly elevated CRP, the nausea and strange bowel experiences, the infectious disease specialist spoke to the gastroenterologist personally and now he wants to do a colonoscopy. Even before this was advised, I had hoped to seek a second opinion from a different gastroenterologist/practice, but unfortunately, a slew of factors (running out of FMLA days/difficulty obtaining short-term disability without a diagnosis; the "re-set" of my out-of-pocket-maximum, which I'd reached in July, on October 1; repair surgery on Friday for an incisional hernia in my umbilicus from my gallbladder removal surgery in 2016; and honestly just exhaustion from feeling like crap) mean I'm pretty much stuck with this guy. So, I need to make sure I'm well educated and know exactly what to ask for and how to prepare. Particularly:

1. Are there any medications that need to be stopped/could affect any potential biopsies taken or testing done (Protonix/pantoprazole, a PPI, especially comes to mind, as well as the antibiotic Doxycycline, and maybe the probiotic)?
2. Is there anything in particular I should ask be done/tested for? I read @tdrell 's note to request biopsies be read by a gastric pathologist (how exactly would you do that? Do I ask the hospital somehow?) and @hokiefan 's suggestion to have stains for eosinophils/mast cells done (not sure what this would be for? I assume some kind of allergy or intolerance?), and I may request an acid-fast bacilli stain done as well in consideration of a positive Quantiferon Gold TB blood test a month ago. I'd like to ask (or if I have time, research beforehand) about whether anything special needs to be done/tested to consider parasites (I had frequent recurrent issues with pinworms as a kid; I've tried the "tape test" and checking my stool several times but don't see anything moving) and/or rectal yeast infection (I'm not entirely sure this is even a thing, but I've been struggling with chronic vaginal "yeast infections" -- the doctors swear that's what's going on and then the culture comes back negative -- so I want to make sure that's not somehow connected. Anything else? Doubting the upper endoscopy results after-the-fact was bad enough -- I do NOT want to have the same worries about this colonoscopy and perhaps have to have it repeated down the road/if I get into Mayo/upon a second opinion).
3. I realize my ignorance is showing, but is there anything gynecological that the gastroenterologist could see/explore in a colonoscopy, and/or anything liver related? There've been a lot of weird vaginal exam findings -- both my primary care and gynecologist were convinced I had a bad, acute yeast infection or (less likely) bacterial vaginosis, and I was started on Diflucan, but then the test results/cultures came back normal, and nobody's given me an alternate explanation other than "practice good genital hygiene", like no douching (never did), I've switched to cotton underwear, I take probiotics when on antibiotics (like I am presently), not sexually active, etc. Admittedly, I've never paid much attention to "down there", and am embarrassingly clueless about what everything is, but from my best understanding of some research (it's actually rather hard to find clear/understandable information on female anatomy that you can match to your own body), I think I have a polyp just inside my vaginal opening. I'm assuming the gastroenterologist can't, and I probably don't want, him taking a peek down there while I'm out and taking any samples or something, but assuming that's true, is there anything he WOULD be able to see/look for that could indicate a gynecological issue (other than the obvious like a prolapse or fistula or something)?

The liver is another thing that keeps coming up with abnormalities; there was a 7x7mm cavernous hemangioma identified and removed from my liver during my gallbladder/appendix removal surgery in 2016, and the biopsy report showed "mixed inflammation of the portal tracts, which is mild to moderate, and contains neutrophils, eosinophils and lymphocytes, predominantly. Foamy histiocytes are also seen in association with the portal tract." I haven't had much luck searching what that means -- my infectious disease specialist didn't think it was normal -- and I don't know for sure that it couldn't all have been from the gallstones that precipitated the surgery, but it's another question. My most recent MRI/ultrasound shows a new lesion, 4x2.7cm focal nodular hyperplasia (benign, but again, I'm 30 years old and not sure why I'm sprouting liver lesions right and left), and one of my abnormal blood results was an elevated LD5, "seen with striated muscle lesions (eg, trauma) and with liver diseases (eg, hepatic congestion, congestive heart failure, hepatitis, cirrhosis, alcoholism)" -- and not an alcoholic, FYI, and hepatitis blood work all came back negative and cardiologist said everything was fine there. But again, if there's anything I can ask him to check out/look for liver-wise, I think it might be a good idea.

Ugh, I always start off intending to write a short, succint post since I know these long honking things scare people off and probably decrease my chances of getting help, but it never seems to work out because there's so many variables or possible avenues to mention, and I don't want to leave out the one little detail that might inspire a lightbulb moment. If you're still reading this, or did a skim the top and bottom, any advice on how to make sure I'm making the most out of this colonoscopy would be greatly appreciated. Advice on how to make this as painless as possible wouldn't be amiss either. 😉 Thanks in advance!

*My main issue was, I asked his office about stopping Pantoprazole (a Proton Pump Inhibitor) prior to the upper endoscopy and was told no need to discontinue. After the procedure, I asked if that PPI use could prompt a false negative biopsy result -- again, was told no; however, all the peer reviewed articles I've read since say in fact it very often does affect the histopathology biopsy (it inhibits the bacteria growth, though you still have it), and should be stopped at least two weeks prior. Also, all the biopsy samples were taken from stomach body, when the evident inflammation was noted in the gastric antrum (and again, research and procedural guidelines seem to instruct taking biopsy samples from both sites). Lastly, the biopsy samples were sent to the pathologist labeled "rule out H. pylori" -- that sounds like it means no other pathology was studied, which seems like a huge waste. On a less technical side, I've also been very frustrated with his lack of communication with me -- right after the endoscopy, he had said I had "watermelon stomach" inflammation very common with H. pylori, but it could also be bile reflux, especially since my gallbladder was removed in 2016; then after the H. pylori biopsy came back negative, and I tried multiple times through his staff to set up an appointment to ask about the PPI use and how we explore bile reflux, and he left a message (I was, ironically, in the bathroom at the time) that "gastritis can be caused by anxiety and stress." That is very true, and I'm not saying that can't be the cause, but I just want to know why the other possible causes he mentioned are suddenly ruled out and the diagnosis is "anxiety". For all these reasons, I'm not thrilled that he'll be doing the colonoscopy, but I feel stuck at this point.