Petrin Hill, Riverside Walk, and Municipal House

For point one, personally I'd skip the watchtower and go to the top of the High Tower attached to ST Vitus Cathedral, much better experience. Then go to the Lobkowicz Cafe, sit on the balcony and enjoy the view over the city.
For point two. I don't know as I haven't got the guide.
For point three you cannot go into the Municipal House historic rooms on your own, only as part of a tour and yes I think it's worth it.

If you like Art Nouveau architecture definitely take the Municipal House tour! The tour gets you into a lot of areas you cannot just wander into, and they are gorgeous. If you have any interest at all in taking photos, pay the (very modest) photography fee. I was very sorry I hadn't done that.

At the time of my visit (summer 2018) there were not very many English-language tours, and I don't think information about the timing was on the website. I stopped by the building on my first pass through that part of Prague and checked on the schedule to be sure I didn't miss the opportunity. I don't remember whether I was able to pre-book the tour; I think I was just told to show up something like 15 minutes ahead of time. Perhaps someone else has a better memory.

We enjoyed Petrin Hill very much. It was a fun ride up the funicular, the views were great and when the restaurant is open, you can sit outside and enjoy a glass of wine. In our case, the restaurant was hosting a private event.

maybe you could post about the riverside walk, done loads of different ones, so if you can let us know where it starts and finishes we can make comment. Kampa island is a lovely area though i must admit Lennon wall just leaves me nonplussed , 20+ years ago it was an interesting feature of the city, now just a place for tourist to write crap graffiti.
as Jason say you must go on an organised tour to see round the Municiple house but worth doing so, there are various bars ,cafes and restaurants in the building all have their merits and all are worth visiting but the American Bar for beer and Becherovka is a favourite stop for me.
As to Petrin tower area, and the cafe Republic, i was quite stunned that they allowed the cafe to be built where it is, the whole area has been completely refurbished and reorganised, nice new toilets but that cafe just ruins any views that you used to get from that area, daresay the views from the cafe will be stunning but why it was built where it is just does not make sense. there use to be places you could get snacks and drinks in the area but all gone now (well gone last time i was there) a favourite place to stop for a beer and sausage but sadly no more. It will only take 30 minutes of your time to go up and down the Tower and well worth it in my opinion. you can walk to the Strahov Monastery area in about 15 minutes from Petrin tower another lovely area and some good bars and restaurants in that area.

@unclegus
Rick Steves' book says to leave Lesser Town by walking across the Manes Bridge to Charles Bridge while walking by Vojanovy Sady, Cihelna, to Kafka Museum, to Kampa Island.

https://www.google.com/maps/dir/Manes+Bridge,+M%C3%A1nes%C5%AFv+most,+Prague+1,+Czechia/Vojanovy+sady,+U+Lu%C5%BEick%C3%A9ho+semin%C3%A1%C5%99e,+118+00+Mal%C3%A1+Strana,+Czechia/Ciheln%C3%A1,+118+00+Mal%C3%A1+Strana,+Czechia/Kafka+Museum,+Ciheln%C3%A1,+Mal%C3%A1+Strana,+Czechia/50.0804434,14.4068871/@50.0845176,14.4056469,15.5z/data=!4m27!4m26!1m5!1m1!1s0x470b94e6feabfcb3:0xc96f6db383ce98dc!2m2!1d14.4126734!2d50.0895647!1m5!1m1!1s0x470b95a3c84ea9d1:0x32be197f3a5c0690!2m2!1d14.4090669!2d50.0888756!1m5!1m1!1s0x470b94e6b94b43f3:0xc35b8e00549059ca!2m2!1d14.4101412!2d50.0885243!1m5!1m1!1s0x470b94e6a2de3243:0x3f7c407c4821f5e1!2m2!1d14.41017!2d50.0882974!1m0!3e2

hopefully this shows it on the map, but it is a short walk (well for me) and you are not actually walking along the river. the Kafka museum is quite interesting if you have read any Kafka and there is a David Cerny installation in the courtyard there that might make you smile.

Thank you!

If you start on the Lesser Town side of Manes Bridge then go into the Wallenstein Gardens. It's open April-October. Then follow the route as described until you get to the other side of Kampa Park. You go up the steps and that's the Legie Bridge. Then you have other options. You could cross the road to keep walking by the river and you'll have the canal locks on your left. At the end of the canal lock is Jiraskuv Bridge and Manes to Jiraskuv takes a little over 30 mins and you get great views on the bridge looking back towards the castle and Dancing House on the other side. Or if you are really adventurous keep on walking under the Jiraskuv bridge and head left so you go right down onto the riverside quay. Then you keep walking along the riverside under the next bridge called Palackeho until you reach a mini boat dock called "Naplavka Smichov". That's a public transport ferry (P5) which takes you across the river (you need a single ticket - service every 15 mins 10am-10pm). Manes to Naplavka Smichov is about 50 minutes.

We are huge Art Nouveau fans and yes, the Municipal House is well worth the time.

We also took an amazing tour with Jason from Living Prague Tours. We took the Prague City Tour. It was the best 2.5 hours in Prague. The tour was very educational, rich in history and an enjoyable introduction to Prague!

https://livingprague.com/tours/living-prague-tours/