Flores is Malaria endemic too. Don't forget to take Malaria prevention pill one week or two week before you go and keep taking the pill two week or a month after you left the place. I forgot the name of the pill that the doctor gave me before I traveled to Flores. I took it two week before and continued three weeks after I returned home, by consuming the pill once a week on the same time (for example every Monday).
Don't forget to bring mosquito repellent with you, wear longs sleeves if possible. Be more cautious when you are in the lowland area.
The local believe that vegetable with bitter taste like Papaya leaves is also good for Malaria prevention (trust me, it's bitter :) )
Hopefully you will not catch Malaria. But if you start feeling the symptoms, get treatment immediately. Reliable hospital can be found in Kupang (West Timor), Maumere and Ende.
But I found good information from St. Rafael Cancar Hospital in Cancar, Manggarai District, and St. Elisabeth Hospital in Lela in Sikka Regency. They also provide information and support in English. I believe it would be useful for international traveler.
Hospital St. Rafael in Cancar, http://www.cancarhospital.com/index.php
St. Elisabeth Hospital in Lela, Sikka Regency, http://www.lelahospital.com/
Try to avoid Ende during your trip over Flores. There's no decent hotels to stay, no attractions, no good restaurants and it's not safe. On your way to Kelimutu lakes stay in Moni - it's very pleasant village in mountains with a few bungalows guesthouses.
I was staying in Ende in Dewi Putra hotel - it's an absolutely stinky hole with broken showers, leaking pipes and shabby bedsheets. I did a mistake - I paid a night in advance (after some bargaining with 30% discount) to some sleepy lazy girl at the reception . After two hours another girl appeared and knocked at my room and demanded to pay 100% showing me a bill. I was really furious because the facilities in bathroom were practically nonexistent and 100000 rp for such a nightmare was too high by Flores standard.
Another local nightmare is a walk after sunset around market. Actually all warungs (restaurants) are concentrated in the market area as well all shameless ojeks (motorbike drivers). They whistle to you, block your way, and if you agree to ride with them they don't mind sexually harass you. I always use ojeks all over Indonesia and only in Ende I was feeling very unsafe to drive with local ojeks.