I agree those things are nice but they are way more than the minimum. eg New crank? If there is nothing wrong with the old crank why change it. Same with the valves. A lot of that stuff is only required if a problem is found. Hence it would be on top of the standard price.
I am reasonably sure Peter is only after a normal rebuild not a performance build. $2K is the right price for a normal build. Having said all that, I do agree with the idea of spending a little more if you drive the car hard. but if not, stick with the standard build.
I also agree with getting written confirmation of the inclusions for that price.
Its a bit like a $999 respray. Nothing wrong with it but when you take the car to them they will find all sorts of add ons that were not identified until they started work.