Hi again Marjan
I can help you with a few of your questions:
You will need to get a bus from the airport into Heraklion bus station (pay on boarding), then get a bus from there to Chania. It will go via Rethymnon, but you will be able to get one straight through.
The link shows the current winter timetable (bottom of page), but this is one which doesn't change a great deal between winter and summer, as it is a basic route used by everyone, residents and tourists alike; I would expect more buses in peak season, possibly scheduled every 30 minutes at some times of the day, but I don't think they will run any earlier or later in the day. In peak season they tend to put extra buses on, all leaving at the same time, rather than extra scheduled times. You need to buy your ticket from the office at the bus station, and you will be allocated a bus number and seat.
The link should update the timetable as the season progresses.
You will see that it takes nearly 3 hours to travel from Heraklion to Chania, so once you add in the time from the airport, and any waiting time at Heraklion, it will be more like 4 hours.
Another option may be a resort transfer service, but to be honest it is unlikely that such a long distance will be available by a shared transfer unless your plane is landing at a suitable time when others want to make the same journey.
If you are arriving before or after the bus service runs, your only options will be hire car or taxi. Taxi is very expensive - it is 150km and costs about €150:
A better option would surely be to book a hotel for your first night in Heraklion, take a taxi there from the airport(€15-20) and get a bus to Chania next morning.
Car hire would probably start at around €30 per day. Presumably you will have too much luggage for a scooter, and in any case I would not recommend that long a drive at night on a bike.
Clothing optional beaches, IMO the best website is the following:
Looks like Georgioupolis and Falassarna may be your best bets, or possibly Kera or Tersanas. Two problems may be that firstly, you are in peak holiday season, and secondly presumably you will be busy during the week, so your excursions will have to be at weekends when everyhere will be much busier, and more likely to be occupied by 'textiles'. Of the 4 I have mentioned, Georgioupolis and Kera should be possible by the bus between Chania and Rethymnon, even if there may be a bit of a walk.
There are clothing essential beaches within 20 minutes walk west of Chania harbour, some of them surprisingly good for town beaches.
Restaurants, I can't do any better than recommend you have a look at the TA 'league table' and filter them out by your price/location requirements:
I would only say, like most places, the restaurants along the harbour are often over-priced, and you are more likely to get a better meal at a lower prce in the streets of the town; however, I have read that a few of the harbour ones are much better than average, so hopefully someone else will point them out to you as well.
I'm sorry I can't help you with your other questions.
Hope this helps
Edited: 5:13 am, February 27, 2012