One other piece of information... I routinely get 41mpg and I drive on ECO like a grandma. I have Goodyear Assurance Fuel Max Tires on the car and basically drive around town. I think the MPG should be higher because I purposely coast a great deal. Perhaps cleaning everything will help. I have ordered a new OEM DENSO Mass Air Flow Sensor and will clean and check the throttle body and EGR valve. Nutz about Bolts is awesome!
Update 8/5/2020 I have replaced the MAF sensor with a new OEM DENSO MAF. I've also cleaned the throttle body. The throttle body was pretty dirty (see pics). I'm going to fill up and see if my MPG changes. It may take a while until the acceleration hesitation occurs again, but I will post an update. Thanks everyone!
I didn't expect to be posting so soon. I just returned from test driving my Prius. I went out to fill up the gas tank, traveling the same road I have for years. WOW! There is a huge difference in performance. The car no longer feels sluggish when I accelerate. It was almost as if I was carrying around an extra 800 pounds. I usually coast to see how high I can get my MPGs and this time, I was able to coast significantly longer without having to use gas - or as much gas. When I returned home from my 5 mile drive, my MPG was 65 mpg. It has never even been close to that. It's always around 49-52 mpg when returning home after filling up. There is a clear difference that can be measured.
The main concern with running your fuel tank low is that the fuel pump is designed to operate while submerged in fuel which cools the pump. When you run your tank low, the pump can get pretty hot, which over time will increase its likelyhood of failing. It's not like running your tank low one time is going to kill the fuel pump, but doing it every time like you do is asking for trouble. FYI: The warning against overfilling is not a just Prius thing. It appies to all vehicles made since the 80s or 90s.