Please critique itinerary

well day 2 is a Saturday and the sites of the Jewish quarter will be closed

Ahhh.....thanks, unclegus! That's what happens when you don't look at the days of the week, lol!

I originally had us visiting the Jewish Quarter the day we arrive but my wife thought that might be too much to take in before our dinner cruise so I'll have to switch Day 2 and Day 3 around........

jewish sites close early on a Friday anyway ,so switching the days the way you are should work fine.

near the Lennon wall is the john lennon Pub, can highly recommend it for lunch.

Just thinking about your day 3 on that list that is now going to be day 2.

cvan I suggest you swap things around.
don't know where you are staying but I would head to the Fennicular at the bottom of Petrin hill, go up on that to the Petrin tower, It is a reasonably easy walk from there to the Strahov Monastery area which is lovely then an easy walk down hill towards the castle area, you will also pass the lovely Loretto building, have a quick look.another few minutes takes you to the castle area,there is security at the castle ,so just head left of the main gates and through security,there were no queues there when I went through last week but be prepared for them.
I presume you will not be doing a tour of the castle area but just a wander through,you can get into the main foyer area of St Vitus and see quite a bit without a ticket. If doing a full tour you really need a full day there. You should be able to get a meal or snack in this area but prices can be on the higher side,there has been some craft and food stalls in the area behind St Vitus last couple of times I have been there so street food might do you.
Once through the castle area head down the castle steps (all very obvious) this takes you to Malostranska metro/tram area and it is a short walk from there to St Nicholas church (never been there ) and from there another short walk to the Lennon wall and finish up at the John Lennon Pub for a beer or two and a meal if you wish.
Doing it this way saves a lot of walking ,much less uphill walking and you will get some great views.
Now the Lennon wall, it is nothing like the guide books, I have a real problem with it being so popular, I remember when it was a area of resistance and protest ,I saw it just after the fall of communism and have seen what it has become . It is a place where any tourist can come along and add their own bit of graffiti. A couple of years ago local art students painted the wall white and left the logo WALL is OVER in the centre of it but since then it has been over-painted numerous times by the tourist hoards, you can sometime see folk selling cans of spray paint to the tourist.,that's my rant over.
Hope this helps.

Your first day is pretty packed. Are you arriving from the US or elsewhere in Europe? I'm asking because if from the US, the evening cruise is going to be tough after changing time zones.

just realised where you are staying,very close to Andel.There is a great metro /tram interchange there and you should be able to get a tram a few stops to Ujezd that stops very close to the funicular .if you buy a 110kc 24 hour pass for the transport system you will be able to use that on both trams and funicular. or a few 24 kc tickets will cover you too.

Thanks for the heads up all - lots of things to consider but we have time to make changes.

From Day 1 I would move Tyn Church to Day 2 as you would include it as part of the Old Town Square. On Day 1 as you have listed the Dancing House then just up the road is ST Cyril and ST Methodius either to visit just the church (free) or include the crypt (Operation Anthropoid) (charge). At the Castle if you can then book places on their "Standard" Castle tour. Licenced castle guide (English Language) takes you on a 60 minute trip through ST Vitus and the Old Royal Palace. 60 minutes doesn't sound much but they can jump the queues so you get maximum time. If you're not sure how this works then just message me and I'll tell you what to do.

Thank you, Jason - private message sent!