What would an advanced amateur charge for an extended family portrait of approximately 40 people.
This is just for the session. And using $8000 worth of equipment?
If you are in the U.S., the price of most photographic equipment is depreciated over five years. That brings your equipment cost to about $30 per week, so if you figure on two or three clients a week the equipment cost really isn't that big of a factor in how you should price your service. Other expenses, such as software updates and upkeep of your equipment won't really have that much of an impact either. The cost of maintaining a commercial studio would be much more significant, but your question doesn't sound like that is the case for you.
You need to be aware of what it costs you to do the job, both in terms of longer term equipment costs (like that $8,000 worth of equipment), as well as short term consumables (like the travel expense to get to the client), and what your time is worth. Allow travel time and the time to do post processing as well as the time actually spent during the photo session. That should be your minimum price point.
What you are really selling is your talent and experience to produce a memorable image. How much that is worth depends on a lot of factors, many of them related as much to the market you are located in as to the quality of the service you can provide. Prices vary widely in different locales, just as the cost of living does. They also vary widely based on the amount of competition in a particular market. This is especially true at the lower end of the price scale. If you are confident, based on your skill and ability to consistently deliver superior results, that you can provide a better service than the plethora of semi-pro photographers delivering semi-mediocre results flooding most markets do not be afraid to charge more than they do.
That's really a loaded question and depends on a lot of factors such as the area you are in, the amount of touch up you will do, your level of experience, the size of the group, what services you will provide in relation to getting it printed, if you are using a studio or doing it on site, etc.
The price of your equipment isn't really relevant to the cost of the service. Your experience and the amount of work you are doing for it is much more relevant. If you are traveling to them and it is the only thing you are doing, the shoot alone would typically cost $50 to several $100 dollars just for the transportation and setup time. If they are coming to a studio, there isn't setup or travel, so it could be as cheap as $10 or $20 or as much as a couple hundred for the actual studio time. That also depends on how much time it takes to arrange them though. If it's a family of 100, it's gonna take a lot more effort and time to get it right. If the extended family is 15, then it isn't such a big deal. This is all based on prices in the North Eastern United States though, it could vary widely elsewhere.
This is basically a pricing question for your service. A quick read here would give you an idea if you want to learn the basics. However, to simplify this problem, figure how much time you spent on the project including preparation and post-processing and come with a figure based on that. I suspect that you do not do this very often so the relationship or the reason you took this endeavour might be more important a factor in considering the amount to charge them. Please do remember that cost and price need not be related.