Doxycycline is indeed effective in West Africa. One advantage it has is that it is much less expensive than Malarone. Children cannot take doxycycline as it can interfere with growing bones & teeth. Your doctor may have wanted to spare you expense by prescribing doxy for the adults.
Mefloquine is also effective in West Africa.
Some notes for you: Malarone needs to be taken with something that has fat in it, in order to be sure the drug is properly absorbed. A meal that includes something fried or fatty meat would suffice. (Full fat milk is good, but unless you know for sure the milk is sterile, you shouldn't be drinking it in Ghana.) Taking it with food also helps avoid upset stomach. It needs to be taken at the same time each day to be sure there is a steady level in your bloodstream.
Meningitis. Take a look at this map: Areas with frequent epidemics of meningococcal meningitis Vaccination is usually recommended only for the dark orange areas. Coastal Ghana is not in that area. The season in Ghana is December-June.
Typhoid:You are some of the unlucky ones who got sore arms. It is not common. The typhoid shot is good for 2 years. If you travel again & need to be revaccinated, tell the doctor about the bad reaction. If the oral typhoid vaccine is available in your country, you might prefer it. Are you sure it was the typhoid and not the yellow fever that caused sore arms? That's a common reaction to YF. Also, if you got all the shots on the same day, then you are more likely to have some soreness.
Thorntree has a Health Branch (where I usually hang out), which is a good place to post these kinds of questions.
