Hi Biswanath,
Ideally you would start this process with a working website to then "templatize" using xforms and workflows and what-not. This is not to say that you cannot do a site-rebuild or re-design in conjunction with a content management effort, just realize that there will be more complexity and will result in a longer project. When we sat down to build alfresco.com we did it in conjunction with a redesign and overhaul of the website. If you take this approach, just make sure to build in extra time for changes as you go along.
Now to answer your questions.
1.) A war file is a convenient way to load a pre-existing content into Alfresco. Another method that you can consider is via ZIP file. I find when I am working and developing a WCM solution that ZIP is easier and more compatible with my development station, so it is my preference. But you can choose what you are comfortable with.
2.) I could envision a solution where Alfresco could manage business logic via a Forms interface. This might be a good integration solution in the future for Alfresco as many rules engines (at least commercial, and OpenSource ones) do take their direction from XML. You could then use an xform to capture the business rules (you would need to strictly define the changeable ones of course), run them through an XSLT or FTL transform and drop the XML in the place where the rules engine is expecting it.
Another option, available now, is to use a commercially or OpenSource available rules engine and just use Alfresco WCM to load content and it's associated metadata (what is required to drive the rules).
That said, right now, Alfresco WCM does lend itself very well to the presentation side.
3.) The only jar files that I have needed to use (and used them to build Alfresco.com) are contained in the virtual-tomcat, common, lib. You should only need to include these in your Eclipse project. Do not build them into your web project. If you export your web-project and need alfresco functions (like the avm) then copy those jars out to the tomcat server in its common lib directory as well.
Biswanath, I hope this helps. Please ask me if you have any follow-up questions.
Brent Kastner