Episode 2 starts off with a set of shots of a Shrine called 一本杉白山神社. Sadly, my Kanji is terrible so my guess is "Ipponsugi Shirayama Shrine".
All Anime images on this post belong to Kyoto Animation, fair use for educational purposes.
We then get to see the exact location of Oreki's house, slightly offset opposite to the shrine itself, except it just happens to be a patch of open land IRL. Additional image credit to Google Streetview, fair use for educational purposes.
Episode 2 also gave me a slightly better angle of Hida Senior High School to compare my own photo with.
The end of episode 2 and the beginning of episode 3 were taken at a cafe named Bagpipe. KyoAni took the liberty of removing the obtrusive lamppost.
Note the attention to detail, with all the clocks and even the retro phone on the pillar being replicated in the anime.
Here is the trollish love clock in question.
The couple's seat. This was a very difficult shot to get, due to a seemingly innocent, but highly obstrusive wall sticking out from the right hand side, seen in KyoAni's version.
As for the food in the Cafe, it is definitely in the very pricey side. The coffee and cake itself were pretty decent, definitely not entry-level things but I expected it to taste a little more special for the price. You're really paying for the great atmosphere and the upkeep of the retro interior here, with its large quantity of vintage clocks. Oreki must be loaded with pocket money since he doesn't do anything other than save energy!
めちゃ高いメニューです！アンチークの時計とかメンテナンス高そうなのでそういう理由なんでしょう。 とても高校生の値段じゃない！ 食べ物は値段的まあまあ普通でした。