Side effects from Yellow Fever vaccination are quite common; their intensity seems to depend on your body mass, eating habits and general condition. In a day or two, they should wear off.
Rabies vaccination is not necessary for the average tourist, but could come in handy if you plan to go stroking a lot of stray dogs, cats and bats; also if you plan to work extensively in the slums of any big city. Btw, the treatment only lengthens the incubation period, it doesn't save you from being infected. If you get bitten by a stray dog, you'd still need to report to the nearest hospital.
Any questions re malaria you better ask Isadora, as she seems to be the expert; this thread may also be of use to you.
It's a bit of a difficult decision on the malaria tablets isn't it! I understand that the most effective course of action is prevention so I will be leaving armed with mosquito net, coils and deet!
I have another question regarding the mosquito nets. I'm thinking of getting an impregnated one but as I've never used one before I thought I'd ask if it's simple enough to hang them up in any hostel/hotel. I'll also be doing a boat trip along the Amazon therefore I need to know if I'm gonna be able to hang one above my hammock on deck or in my cabin if I choose to sleep there instead.
I'm not a big fan of mosquito nets; they are fragile, and even the tiniest hole will render them useless. Hostel bunks don't often provide an easy way of installing them, either. But íf you decide to buy one, best take an impregnated one, as the plain versions are even less useful.
Instead, use DEET-based insect repellents (don't forget your hands and feet), or sleep with a ventilator turned on. Either helps just fine.