How to stay longer than 3 months in Europe?

Your basic info is correct, England is separate from the Schengen zone, you have 90 days, they do not need to be consecutive, but you are limited to 90 days in any 180 day period.

Your cruise is a wild card, it depends on how passports and entry are handled. On some you are on your own passport, on others you are issued a "day pass" for lack of a better word and your passport remains on the ship, so you are not technically entering the country just transiting or visiting for the day on the ships visa (Turkey does this, not sure how many other countries).

I would assume the worst case and that the days count. Keep in mind any part of a day in the schengen zone counts as a day, get there just before midnight...still a day. Also not a good idea to try and cut it close to the day of 90 days, in case you miscount.

Check what the State Dept says, also.
http://travel.state.gov/content/passports/english/go/schengen-fact-sheet.html

"If you are a U.S. citizen with a valid U.S. passport traveling for tourism or business, you can apply to enter the Schengen area without a visa for a period of three months within each six-month period. If you spend three months in the Schengen area during any six-month period, you must wait another three months before you can apply to enter the Schengen area again without a visa. If you do not meet these conditions, or plan to stay in the Schengen area longer than three months, contact the embassy of the country where you plan to spend the majority of your time to apply for a visa."

Needless to say, again State has it WRONG. It isn't months. It is days. 90 in any 180. 3 months can be close to 90 days, but not exactly. Follow the rules as you have described.

The 40 days in England doesn't enter into it. In fact, in most cases you can have up to 180 days in England with no hassle.

The 90 days in the Schengen area include any time spent there. Even if the passports remain on the ship there is a chance that the authorities have been provided a list of passengers going ashore. Don't risk it.

Subtract the days that you were in Dutch and German water and on land there from your 90 and that is how long you will be able to remain when you go to the Continent.

When you go between Germany or France and Italy if you transit Austria or Switzerland those days count too as both of them are also parties to Schengen.

Ships, as well as aircraft, provide both a pax and crew manifest to the authorities at every country in which they dock/land. It's transmitted well prior to the vessel's or aircraft's arrival. It's another means of identifying buttheads of interest. Prior transmission is not required for corporate or private conveyances but must be delivered prior to debarkation.

They may provide a list of debarking pax whose passports remain on the ship, but it varies by country.

I've no idea if debarking day visitors' scoop is entered into an immigration system.

I do not think there is a mention by anyone, all I can add is and you may have already this common sense - you should keep any documentation proving your entries and exits have not exceeded ninety days in the Schengen zone.

Thanks to all that replied, I got my answer that I need before booking. I shall be a fan of travel forums from now on. Happy travels to all , no better way to spend your money and learn ! Like the Brazilians say " the coffin does not have drawers so enjoy your money while you can "