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<hr>Compared to London it was very dirty and hideously expensive. <hr></blockquote>
every cost of living survey as well as my personal experience (visit london once a month from Paris) says exactly the opposite

London is way more expensive than Paris. No doubt about it.
I agree you're packing too much on day 3. Don't miss Sainte Chapelle, certainly the most beautiful church in PAris.

Given that you in fact have only 2 and a half days in Paris, I would skip Versailles totally.
I agree with the other posters who say you should be outside if tired and jet-lagged rather than in a museum. Museums are tiring under any conditions, with slow walking and stopping and crowds. At least outside, you will be able to stop and sit down at a café for a drink if you are tired, and you have the street and people to look at while you are resting.
If you absolutely want to go to a museum, go to the Musée d'Orsay rather than the Louvre, unless there is something really special you want to see in the latter. Check in your guidebook about museum opening days too. Traditionally, they closed on Tuesday, but some might be closed on Monday instead.
I think one of the great pleasures of Paris is walking around and discovering unexpected buildings, shops or nice views. I understand you want to see a maximum number of sights like Notre Dame, but would personally skip the Pantheon and Invalides. So instead of rushing from one place to another by metro, check your map to see you are going in the general direction of your next destination, and walk or take a bus (costs one metro ticket and the itineraries are posted on maps on every bus stop).
#10 I agree about London.

Yes - certainly skip Versailles. Move Louvre from day 1 (you do not have jet lag at all? not even for a few days?).
Althogh the metro system is fast and efficient do not undreestimate the time to get from A to B - rarely less than 1 hour. (finding the station, waiting for a train, driving, getting up from station, finding your way to "B").
Honestly I think you can only make approx. half of what you plan - and there is NO time to look at thngs more than 10 minutes, to sit on a cafe and watch bypassers. When are you going to enjoy some fabulouls meals on good restaurants? Or try to get away from the most touristy areas and see a bit of paris proper?

You will save time at the Louvre if you don't go up to the pyramid entrance, but rather downstairs via the metro entrance where there are fewer people.
The bateaubus goes about every 20 minutes on the Seine and stops at 8 useful stops along the way - includes Notre Dame, Louvre, Eiffel tower, musee d'orsay, Jardin de plantes. Start early and you can get off where you want and rest between times.
Don't try to do everything in 3 days. Perhaps you don't have to be together all the time and could sample different things.

As others said, don't bother with Versailles - stay in the city for a 3-day jaunt.
Ste-Chapelle is a much more interesting church than St-Sulpice. I do hope you weren't planning on the latter because of that dreadful, leaden book that became a still more dreadful film.
Are you staying in the Latin Quarter? You should just walk around there, perhaps drop in at Musée de Cluny (for the building itself as much as the tapestries and other medieval art) on the first day. I also notice that you don't seem to be exploring the Marais or the Bastille area (that is also on the right bank). Just look at Sacré-Coeur from the outside - the view from its esplanade is nice, but it is a late 19th-century eclectic monstrosity, not an ancient church. You'll find older and more interesting churches than that in Québec or Atlantic Canada.
The bateaubus on the Seine is a good idea, though also, dreadfully "touristy" though it might be, why not take a bâteau-mouche? I did it with a friend who was visiting me one time I was working in Paris, and it was a hoot. The illuminations in the evening are especially pleasant - don't waste your money on a boat with meals, just take the plain boat and enjoy a late meal afterwards.
Why such a short stay - are you heading elsewhere in Europe? Three days is a very short stay for crossing the Atlantic.

Provided you don't eat, drink, use public transport or stay in hotels, London can be cheap compared with Paris.

One thing I like about London is the free museums. But it being cheaper than Paris is ludicrous.
Anyway, Ste Chapelle is being renovates, so there are scaffoldings on the sides. But you go there for the stained glass so not a problem. Just go when it is sunny..
I wasn't able to see it in ideal conditions as I kept on posponing going in due to the crowds. It is still great but I'd imagine it'll be stunning with the sunshine.