As with any trip it is important to look into the health side of things before making any further plans. Komodo and Flores being tropical locations within Indonesia are subjects to risks from a variety of illnesses although there are effective precautions you can practice in order to minimalize the risk of running in to any of them. The first and maybe most obvious thing to mention is to pack a good first aid kit and make sure you are well equipped with and medications and treatments that you and anyone on the trip already requires, these may include prescription drugs and lenses. It is often wise to pack at least two sets of these in order to prevent lose. 

A visit to your doctor or a recommendation for a consultant who specializes or is experienced with tropical medicines is essential to inform you of the specific requirements and risks that you may run into. It is wise to do this at least 4 to 8 weeks before traveling as some drugs and treatments have a waiting period before they are effective. You may also need to talk about any existing illnesses particularly heart problems the effects that traveling may have. Insurance is an extremely good idea as nowadays it is very cheap and a good plan will cover all your health needs as well as general travel issues with exceptions that are usually reserved for extreme activities and silly behavior such as driving after drinking and rock climbing. It also wise to consider over seas costs and availability of any medications you may require. 

Vaccinations may be necessary depending on your travel and vaccination history, again a tropical expert is required and it is important to consult this person well before booking flights and making other arrangements. 

Recommends by the World Health Organization (WHO) include vaccinations for adult diphtheria and tetanus, measles, mumps and rubella, hepatitis A, hepatitis B, varicella, polio, typhoid, rabies, meningitis and tuberculosis. These are recommendations standard to the whole of southeast Asia, you may not be in contact with all off these depending on what your travel plans are.

Malaria is a risk in some areas and some times of year although many cities and less remote areas an be extremely low or no risk areas, Malaria can be treated by a variety of drugs although some have reasonable strong side effects, consult an expert with up to date information on whether you need this as the modern drugs are much better although it is worth avoiding the drugs if possible. Dengue fever is another mosquito transmitted disease that is milder than malaria and has no real treatment other than rest and hydration. It is rare and unlikely you will get this on a short trip but mosquito avoidance measure include using a 'Deet' based spray, wearing light coloured clothes, mosquito nets and coils extra.

Rabies and hygiene issues are also to be considered although there may b 0 risk of Rabies in your area. The only real common illness is an attack of the runs which is likely to get you at some point, just stay hydrated, see the funny side and this will pass. Besides people pay huge amounts of money in SPAs for far less effective toxin flushes!