9 days in total. 4 days in Tokyo, 3 in Kyoto, 2 in Osaka.
ah, I see. well, a few things to keep in mind.
first, you WILL get lost in the subway stations. just a matter of how long are you lost down there depending on your sense of direction. so any place you're going, add some additional time over it so you're not totally rushing. and keep in mind the trains and subways are on time most of the time. we're talking about only late or early by maybe 10~30 seconds, so never cut your timing too close if you're going to catch a connecting ride.
second, are you flying out from Osaka or going back to Tokyo first? if you are flying out of Osaka, I would strongly suggest you to just buy the regular Shinkansen ticket going from Tokyo to Kyoto and comboing it with a Kansai JR pass instead of buying the full regular JR pass. that should save you quite a bit. and when you're in Tokyo, there should be day passes from all the private railways if you're going to use them a lot any particular day, so go with those.
and of course you will walk. a lot. and not just walking, you'll also do a lot of stairs. most stations do have elevator, but it's often just that one single elevator on the side of the station opposite of where you're existing, so stairs is the fastest way you will be getting in and out of there. September will probably still be pretty hot, so have a small towel or handkerchief with you to wipe down from time to time. I know you're from Vegas and it's been over 100F continuously for the last 2 months, but the humidity will make this a totally different kinda thing, so keep that in mind. hell, if you're prone to sweating, I would recommend some strong deodorant and maybe even baby powder, if you don't want to look like somebody just dumped a bucket full of water on you 15 minutes ago all the time.
I'm going to guess you don't plan on going outside of Kyoto and Osaka during the time you're in those cities? you will have plenty on your hands even just in these cities with the time you have. especially with the huge amount of tourists there, you will probably have to wait in line pretty often too, so always have that in mind if you plan on going anywhere that requires getting tickets or have long lines. do you already have some places you have in mind? try to map it out so you're going to all the points of interest in that area in one go. for example, Kinkaku-ji (the golden one) and Ryoan-ji (the one with the famous Zen garden) are somewhat close by each other, so you can go to those places together. and I highly recommend you go to some areas as early in the morning as humanly possibly. places like Fushimi Inati Taisha, Kiyomizu-dera and Arashiyama Bamboo path. mainly because these locations are best experience without 15 people breathing down the back of your neck once it's after 9am. but if you don't mind the crowds, don't then worry too much about it.
as for the famous markets, yes they're all overpriced these days due to tourist. Tsukiji in Tokyo, Nishiki in Kyoto, and Kuromon in Osaka are all the same. are they still worth going thou? I think so. you can still find some good food and fun experience there. just don't go for some obvious tourist traps like the wagyu beef skewers or the ¥5000~¥7000 seafood bowl. the former, even if they're real Kobe wagyu beef, without the proper skill to cook them, it's just a waste of money. the later, the ingredients might be good, but you will be able to find some equally good ones at some local small eateries at probably a much lower price. if you're going there, go with the tamagoyaki or one of the seafood BBQ stuff. maybe even the hot press seafood crackers. btw, do you plan on visiting Toyosu Market? it's the location that the old Tsukiji Market had moved to. you will be able to see the tuna auction in the morning if you go early enough. and now it doesn't require you to get in line at 2am in order to get in one of the 120 spots that day for the viewing. you just have to go at between 5am to 6:30am and freely watch it out of the 2nd floor windows. and afterwards you can even go for a freshly hand make sushi breakfast if that's the kinda stuff you like. I have some recommendations if you're interested in those.
but most important of all, try things that interest you and tickle your fancy. don't worry about making mistakes (as long as you don't be a jerk) and don't just blindly follow my advice. everyone likes different things and all situations can be different, but as long as you're sincere about it, most people there will understand and help you the best they can.