London to Normandy and a few things in between

Dover and then take the high speed to Calais

Can't be done. The Channel tunnel starts near Folkestone, but the last train stop is Ashford, and very few trains stop at Calais Fréthun, which is well outside Calais town. You would need to get a train from Ashford to Lille, and there are only two of those per day.
Timetable here: http://www.eurostar.com/sites/default/files/pdf/timetable/UKEN%20Timetable.pdf

Take train to Plymouth then Ferry to St Malo

No need to go that far west. There are ferries from Portsmouth to Normandy, see here: http://www.brittany-ferries.co.uk/ferry-routes/ferries-france/portsmouth-france
And there is enough to see for a part day in Portsmouth.

Two countries in 10 days -- all right, go for it! I can't comment on Option 1 as I haven't gone that route (well, at least not for many many years). In light of what the previous commenter says, you'll be wise to research which ferries run from which ports on which days. They don't all run every day, especially during the off season and "shoulder" season.

Option 2 is certainly more direct and puts you much nearer to Mont St Michel, so if MSM was my priority I'd take Option 2. Do be aware that the cross-channel ferries can have last-minute cancellations for a variety of reasons (labor dispute, mechanical trouble, political disturbance...). You might find out on short notice that you need to depart from, say, Poole instead of Plymouth and land in Cherbourg instead of St Malo. Not trying to scare you -- it is quite unlikely that this would happen -- but I'm advising that you call ahead to confirm and make sure the ferry company has your mobile # to text you just in case. It happened to us and the ferry staff and rental car company were very helpful.

The advice about taking the ferry from Portsmouth is a good one. In addition as you clearly have an interest in DDay there is a very good DDay museum in Portsmouth plus there is a lovely village on the outskirts of Portsmouth, Southwick, which is where the DDay invasion was planned. Southwick House is where Eisenhower and Churchill stayed and you can visit by prior appointment.

I wouldn't bother with the Cliff's of Dover, they're just cliffs and there are plenty of them around the UK, there's even some in Portsmouth although I admit they're not quite so iconic or impressive. I would suggest taking the train from London to Portsmouth, spend a day or two there and then take the ferry to Cherbourg. From Cherbourg it's just over an hours drive to Bayeux.

I'll just add if you do come in at Saint-Malo stop and see this charming town. I'm visiting right now and it is really interesting with the walled city, the beaches, the impressive tide change, the long history of the corsairs/privateers.

Cancale, an oystering center with a charming harbor front, is on the way to Mont St-Michel from Saint-Malo.

I'm not a huge MSM fan but I do like Saint-Malo a lot!

No advice on the ferry/car thing, so take the advice of others on that.

I like Option 2. If you can squeeze a night or two in Caen, the museum there is worth a day. It made the whole trip to the beaches come alive.

Another vote for option 2. There is normally an overnight ferry from Portsmouth to St Malo, with lots of sleeping options ( check Aferry.com for schedules ), which arrives early in the morning. You could visit the naval museum, have a late dinner in Portsmouth, then sleep on the ship.
The last time that I was in St Malo there were several car rental counters after you clear customs. You could then visit Mount St Michel and get to Bayeux in the evening for 3 nights ( there really is a lot to see in the area ). A car makes everything in Normandy much easier. I would then drop off the car in Bayeux or Caen and take the train to Paris.
Thus 4 nights in London, 1 on the boat, 3 nights in Bayeux and 2 in Paris.
Enjoy!

Don't go to Plymouth; go to Portsmouth - it's much closer to London, just 90 minutes on the train, and you can get to Caen, Cherbourg or Le Havre via Brittany Ferries. http://www.brittany-ferries.co.uk/guides/france/normandy

Many people, even Brits, get Portsmouth & Plymouth mixed up - so I just wanted to check that you choose the closer option, otherwise it's 200 miles extra down to Plymouth!

Thanks for all the great advice. I knew the train didn't leave from Dover, just planned on staying there and seeing the cliffs because it was in close proximity to where the train leaves from. And Lille would be fine for the arrival.
I guess I was also wondering if the longer drive rather than the longer ferry would be worth the cost savings? And maybe there is something wonderful to see on that route. However all of the advice does seem to point towards my option of ferry from Plymouth or Portsmouth.
Also loving the option of the closer ferry in Portsmouth to Cherbourg! Thanks again

Here is a rough, emphasis on rough! itinerary.
We have booked flights for late Sept. My first time in London and England, Hubby's third.

Day 1
Arrive London morning, not planning much here as I know I am normally kinda shot after a red eye.
Will probably take in the area we are staying, and maybe try to hit one site close by wherever we stay.
Lodging suggestions/area's welcome.

Day 2
Tower of London then Thames cruise
Lunch recommendations?
Tour Westminster, stay for Evensong (not sure if this is every night, and I believe I need advance tickets?)
Maybe Picadilly Circus or Harrods in the evening Hours?

Day 3
Side trip to Stratford and Warwick Castle, doable? Worth it?

Day 4
London Bridge
Globe theatre
Tate Museum

Day 5
British Museum
tea somewhere fun?
See a show

Day 6
Travel Kensington Gardens or Stonehenge on the way to Portsmouth. Sleep Portsmouth, thoughts?

Day 7 Ferry to St Malo- pick up car
Mont Saint Michel
Drive to Bayeux - sleep Bayeux

Day 8 Normandy - D-day sites sleep Bayeux again. Possibly see Tapestry's one of the days.

Day 9 drive to Rouen and or Giverny on way to Paris. Best place to drop car and train into Paris?

Day 10 Paris- a few sites we missed on last trip ( we have both been to Paris)

Day 11 More Paris sites, still unplanned.

Day 12 Fly out afternoon

Other sites interested in, Buckingham Palace- don't care to see the changing of the guard. Highclere Castle, great restaurants, beautiful gardens. Would be interested in seeing a play at the Globe possibly. Any other must see sites I am missing?
Not really interested in London Eye, or Churchill War museum ( hubby has been there)

Brenjay, I will address some of the questions in your last post.

"Day 1
Will probably take in the area we are staying, and maybe try to hit one site close by wherever we stay.
Lodging suggestions/area's welcome."

Do you have any neighborhood scoped out which appeals to you?
Do you want a hotel room, B&B, or apartment?

"Day 2
Tower of London then Thames cruise
Lunch recommendations?"

The Tower of London has an excellent lunch room, The Armories Cafe. They serve plate lunches, sandwiches, salads, desserts, and pastries. I'd suggest getting something there for lunch after you finish touring the Tower of London. It is inside the Tower of London.

For your cruise on the Thames, you are perfectly positioned once you finish touring the Tower, to go to the nearby Tower Pier and hop on a Thames Clipper boat., which take the Oyster card as a form of payment. Just tap in. The boats travel east on the river to Greenwich, and west to Westminster Pier, near Big Ben, Parliament, Westminster Abbey.

"Tour Westminster, stay for Evensong (not sure if this is every night, and I believe I need advance tickets?)
Maybe Picadilly Circus or Harrods in the evening Hours?"

I believe you do not need tickets for Evensong. If that has changed, I'm sure someone will jump in and correct me.
Especially if you have just paid to get into Westminster Abbey. If you stay that long, just take a seat in one of the pews and wait for Evensong. Westminster Abbey has a cafe for sandwiches, snacks and refreshments; so you could grab something to eat after you've toured the Abbey, and to kill some time while waiting for the Evensong to begin.

Piccadilly Circus is a busy traffic intersection. Not much to see there but traffic and some neon large advertising signs. You will go through there on a Hop-On-Hop-Off bus tour if you take one, or on one of the regular city buses used for transport around London. Skip Piccadilly Circus and go to Harrod's and get that over with.

"Day 3
Side trip to Stratford and Warwick Castle, doable? Worth it?"

It is do-able. You would take the train out of London, get off at Warwick to see the castle, get back on the train and continue on a very short distance to Stratford-Upon-Avon. Warwick Castle will take half a day, Stratford-Upon-Avon can be done in half a day. Train back to London in the evening.

When checking train schedules or buying train tickets, refer to Stratford-Upon-Avon by its full name. There is a Stratford in England, but it is not the same town.

You asked, "Worth it?" My opinion is that both are worth it.

"Day 5
British Museum
tea somewhere fun?"

The British Museum has a cafe which serves a great tea. This way, you can take a break from looking around the museum, have tea, then resume seeing the museum.

I'm sure others will chime in with great suggestions for tea around London.

"Day 4
London Bridge"
I think that you probably mean Tower Bridge:
http://www.goandco.co.uk/images/offices/tower-bridge.jpg

London Bridge:
http://www.walklondon.com/london-walks/walk-london-images/pool-of-london/london-bridge-att3.jpg