Include it all, but break up the proposal so it seems like they're getting a good value for the money.
With a project like this, it's important to have a rough guess as to what you can charge your client without making them squirm. It's also important to take into consideration who you are, and how they percieve you. It's one thing if you're a top-tier studio with fortune 500 clientele, and it's another if you're Johnny up the street with a thin portfolio of past work.
Here's how I work these things out - I come up with a hard number I feel comfortable with - take $2,850 for instance. Then I assign myself an hourly rate that seems reasonable, dependent on the client's expectations. Then I create a proposal, projecting my time onto the following steps:
• Content Evaluation
• Research and Conceptualization
• Resource Collection and Production
• Content Structure
• Production
So, in the above example, let's assume that we want to charge $50 an hour for our work. That means 57 hours of work. I'd create a proposal assigning a time estimate to each of these categories totaling up to 57. At least half of your hours should be under "Production", since that covers everything from Flash to Backend stuff.
In the end, you'll be doing lots of work on the site, so there's nothing wrong with demonstrating that on an invoice. It can be a turn off if your client sees a proposal that's just a page with your monogram and a big number.
In any case, ask yourself if this client is likely to refer others. If so, then give yourself some breathing room with in your estimate. If not, then go for the gusto, but keep in mind that you shouldn't superceed the impression you've made on these folks.