There is a trickle of tourists starting to come to East Timor to get their Indonesian visas again.

The Backpackers Guesthouse in Dili is the best place to stay while you are waiting for your visa. You can take the Timor Travel shuttle from Kupang to Dili for less than 20.00 USD - 170,000 rupiah) and they will drop you at the guesthouse. It takes all day and you will arrive at night.

Be sure to get the 30 day visa for East Timor at the border. Even if you only plan to stay a few days because there are  fines for overstaying your ET visa and you might want to stick around for a while.

When applying for your Indonesia visa you will need a photo. The visa costs 35.00 USD and usually takes 5 working days except under special circumstances it can be done in less time. It usually requires writting a letter in Bahasa Indonesian.

Dili is a good place to make your visa run if you are in Eastern Indonesia. 60 day visas can be had if you do the paperwork properly and have a sponsor in Indonesia.