You DON'T "calculate" her rate, SHE does. You propose to her what you want to do, she tells you how much it costs, you decide if you can afford it. If she is open to negotiation, go ahead.
There is no standard protocol for transportation. Just ask her what she wants to do.
I don't know what you mean by "what should I avoid".
As already stated by others, SHE sets the rate, SHE decides what she is comfortable with as far as transportation, and SHE sets the limits.
All that said, you mention she is new to the business, so it is possible she has not thought this scenario through and made decisions regarding all this. It is possible she is not prepared or willing to do an overnight at this point. It is also possible she is comfortable enough with you to openly discuss it.
IMHO the best approach would be when you see her this week. After "play time" when you are both chilling, ask something like "I really enjoy when we don't have to rush through our to time. What do you think about spending the night together sometime?". If she is receptive then the door is open to discuss all the issues.
Be prepared to gracefully accept her saying no thank you.
1) This varies widely. Some providers outline rates for specific time blocks and state certain limits. For example, "12hr overnight $1800 - includes 4 hours actually sleeping".
2) If she is savvy, she will have transportation available. Looking at it from a providers POV, I would not like to be "trapped" somewhere if the date went south.
3) In the morning, I would seriously avoid cooking bacon and eggs naked.
