In the clutch section ( http://www.nsxprime.com/FAQ/Troubleshooting/clutch.htm ) it shows prices generally around $2000. In most cases it doesn't break out parts vs labor but I think labor is anywhere from $500 to $800. Based on that I would guess something around 8-10 hours, give or take.
You should not be charged for multiple work. A clutch rebuild on it's own may take a certain amount of time and cost that much. However, that includes disassembly to get to it, the work, and reassembly. Since you are doing a number of other things in that area which will already have the tranny apart, it should reduce that amount considerably. They should only charge you in hours, not for a standard clutch job. That would be simply unnacceptable and if they try, don't stand for it.
You can't get charged for hours of labor that did not occur.
I had my clutch replaced a couple of weeks ago, the initial estimate was $590 for the labor only (for a 9hr job!) I ended up paying more than that, additional charges included $99 for a 4 wheel alignment.
I think the service manager was trying to do me good then realized he wasn't covering his costs and needed to add the additional labor cost, total amount for the clutch work was $780.
I think most labor rates for the NSX are pretty accurate. I have known other shops to work on other types of vehicles and if they quote 3 hours from the book and it only takes 1 1/2 hours to complete, you STILL get charged for 3 hours of labor. They probably justify this for the jobs that end up taking longer than the book indicated and ended up losing money on the job.
That's how the 'book' cost system is supposed to work. It rewards experienced (faster) mechanics, who then make more money, and underpays inexperienced (slower) mechanics. That way shops don't have to work out complex sliding pay scales for mechanics of different abilities.