#3. Could anyone tell me the best area to stay in Paris to accomplish the above Eifell and stroll Si

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I am like dsauna, planning a trip through Italy in France except mine will be in late September into October of 2013, a honeymoon, around 22 total days, meandering through France and Italy and not knowing quite where to begin. I figured because France was cooler, I'd begin there and that way could still enjoy some warmer weather, even lay around on beach by the time I ended my 21 days in Amalfi area. So this leads me to Question #1.
1. Is this an okay time of year to plan to start in Paris Mid-September and end in Amalfi around October 5? As far as weather is concerned, is there any rainy season I should expect? And, Will it still be warm enough to swim in Amalfi the first week of October?
I will note that we Arrive Paris early morning stay 2 full days and nights-our only goal is to do the Eifell Tower at night and stroll along the Siene and have a romantic dinner. Not museaum folks and not shoppers, been there once way too expensive!
#3. Could anyone tell me the best area to stay in Paris to accomplish the above Eifell and stroll Siene that would also be located nearby the train in from the airport what cruise lines sail from seattle to alaska and a train that could get us to our next place which would be either Nice or Marseilles? whichever one is logically next.
#6. Would it make sense to buy a tour package for any part of the trip, I was considering it for the first part of the trip starting in Paris and as far and even down as far as Cinque Terre or Venice, since I have places I really want to stay in Tuscany (after Siena) and again in Amalfi? Can anyone recommend a reputable tour company for such a thing?
Although some people drive into Rome to return a rental car, I would drop it in either Chiusi or Orvieto and train into the city. However, this plan doesn't work if you're returning the car on Saturday afternoon or Sunday when rental offices in Chiusi and Orvieto are not open. (You would also not be able to pick up a car in Siena on Saturday afternoon or Sunday.)
Back to public trans... There is a bus from Rome to Sorrento, but if you wanted to stop at Pompeii on the way you'd need to take the train to Naples (some as fast as 1:10 hours), transfer to the Circumvesuviana commuter train and go another 30-35 minutes to Pompeii where you can store your luggage at the main entrance. Then it's another 30-35 minutes to Sorrento.
I don't think going to Ischia what cruise lines sail from seattle to alaska from Amalfi for only one night makes sense, what cruise lines sail from seattle to alaska but check the ferry schedules. I believe you'd have to first go to Naples. I would probably re-order this part of the itinerary to put Sorrento at the end so that you have more reliable options for getting to the Naples airport for your outbound flight. If the Ischia-Naples ferries are briefly halted for weather or other reasons, you could miss your flight.
Since you're somewhat ambivalent about Paris and Rome, I'd drop them from the itinerary and add the days elsewhere. Venice in particular is a long way to go for only one full day of sightseeing. If you keep Rome in the mix, don't stay near the train station. It's probably the most charmless part of the city.