I'd check with your own practitioner, and AME but:
In short getting the disease is worse than having the jabs. The quoted reputable side effects include; jabs - pain and swelling at the injection sites, mild fever, allergy to the injection(you'll notice pretty quickly). Malaria prophylaxis; GI upset (tummy pain, vomiting, diarrohea), headaches, nausea, tiredness, allergy to the meds. You also need to be taking the meds for a short while even after returning - so you'll need to tell your AME (and therfore not be able to fly for at least a month-while taking them)
Something which would be useful is to actually find out whether you are going to be at risk of getting these diseases. ie whether it is the season for the nasty insects, which carry the diseases, to be biting. The other is to make sure that you take precautions against getting bitten, ie insect repellant. And to make sure that you are aware of other diseases which are prevalent where you are going and how you can catch them, ie HIV AIDS etc.
I nice website which I use frequently is
www.GPNOTEBOOK.com
The other website is the Dept of Health website