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According to what people say it shouldn't be too difficult to cross the border overland if you get your visa in advance, or in Kupang/Dili at the latest, before heading to the border. You don't have to wait for the visa as long as you did a couple of years ago, but I can't quote any exact source for you at the moment.

Hopefully, TransNusa will open up their international routes from Darwin and Dili to Kupang as planned.

http://www.antaranews.com/en/news/83456/transnusa-open-flight-route-to-connect-kupang-dili-darwin

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This event took place two weeks ago. Love it. http://www.tourdetimor.com/raceday/

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Thanks for posting me this link. The pictures are awesome.
A reason more to go there.

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There are three companies running multiple buses on the Kupang-Dili, Dili-Kupang run every day. Timor Tour & Travel, Paradise Travel, and Valley Desert Travel. They are fixing the road on both sides of the border at the moment. The travel time between the two cities is currently about 12-13hours by bus. West Timor is GMT +8, Timor-Leste is GMT +9. If you pay for this service, it is about $21, the buses don't cross the border, they have a twin bus on the other side of the border that you will change to after you have passed immigration.

If you want to cross by land from West Timor (Indonesia) to Timor-Leste, you first need to first obtain a free 'Authorization' letter from the Timorese consulate in either Bali or Kupang. This will allow you to exit Indonesia and buy a Timorese visa ($30) at the border.

Both Merpati and Batavia fly from Dili to Bali. The price is about US$130 each way. If they tell you in Bali that you must have a return ticket, they are lying. It seems to be Merpati mainly feeding this BS. A return ticket is not needed for a Timorese visa. If you fly into Dili, you can get a visa on arrival for $30, no authorization needed. The visa you are given at the land border or on arrival is the same. Both can be extended for another 60 days while in Timor-Leste. After 90 days you must leave Timor-Leste.

There is a main road running through West Timor, from Kupang to Atambua. It is fully paved (except where they are currently resurfacing it), mostly one lane each way, sometime two lanes each way. The roads in West Timor are okay to any place you would ever want to go to. There are two routes to go from Atambua to the Timorese border. The buses seem to be using the longer, but more scenic and comfortable route via Atapupu at the moment.

There is a branch of an Indonesian bank at the border. They advertise a money change rate and have an ATM. I have never seen anyone use them. If you are coming by bus. The bus companies usually have their own money change desk in Atambua that has a reasonable rate. You do need $30 in US cash for the border. I've given $40 and $50 and they've given me change, but it is much easier if you have $30 in change.

On the Timorese side they have just opened the new border / immigration buildings, so things are still working themselves out. Have a pen, it makes everything easier.

I would say there are no more risks for lone females in Timor-Leste than in Indonesia. I'd probably say due to the larger amount of foreign (malae) females in Timor, it is a bit safer than Indonesia. This is a very catholic country so you will find that Timorese women often dress more conservatively, but you will see many Timorese women wearing short shorts. Timorese males will often misinterpret a foreign womans revealing clothes as a more relaxed attitude to sex. Often a stern 'NO' is all that is need to send them running.

Most diving in Timor-Leste is shore diving. The coral is Timor has not been affected by dynamite fishing as it has in certain parts of Indonesia, so it is untouched If training, the prices are probably higher than in somewhere such as Thailand, but the three companies running in Timor are more into it for the beauty of the diving here in Timor, not just the money. As the wet season comes, you will find that the visibility is reduced immediately after a heavy rain, but it is still good.