Ferry from Flores to Timor
The Flores-Timor sailing is much more infrequent than the other island hops on the route between Jakarta and Dili. Instead of a minimum of one per day, you are looking at one or two sailings per week.
If you want to experience the journey outlined in the diary section, then call at Aimere and take the Perum ASDP sailing. While on this boat, if you don't want your vehicle to be used as a dormitory, take a large pot of extra-strong coffee to counter the sleep-desire, a thick book to pass the time, and a cattle prod.
If you want the more civilised approach, Ende is your port.
When I called into Ende, the two different companies had one boat each from Ende to Kupang, which both left within hours of each other (11pm Friday night for the "new" boat, and Saturday for ASDP). Hence the reason for me sailing from Aimere. I'm not sure if this is a weekly schedule, or a rolling schedule which just happened to result in both sailing together when I was enquiring.
The "new" boat is the KM Kirana II. It is operated by a company in Ende, on telephone 0381 21927. Their office is on the road leading to the port (Ipi), about 100m from the harbour office on the left-hand side. They do not speak English in this office. On the brochure, their vessel seems new, and more like a European long-distance ferry, with cabins and lounges. Rather different to the floating cattle barge run by ASDP from Aimere.
ASDP have offices at every port throughout Indonesia, so check at a few of their offices on the way down to find the sailing schedule for Ende-Kupang. Don't rely on one set of information though - check at a number of different offices.