Hi Mama,
While 99.8 - 100 degrees is not a worrisome fever in terms of acute illness or infection, it's still a low-grade fever if it's at least 1 degree above his "normal" temperature, and it's unusual to run an above-normal temperature for two weeks. You probably should talk about this with his pediatrician. There could be an underlying health issue brewing (many auto-immune diseases will first manifest with long-term low-grade temperature elevation), but do keep in mind that these are pretty rare conditions.
A less worrisome possibility is that, given that you live in a very hot place, your son's body temp is slightly elevated because of elevated environmental heat and possibly mild dehydration. Try keeping him cool and make sure he drinks plenty of cool fluids for a few days, and see how his body responds. Humans are pretty good at regulating body temperature, but temperature can still elevate in response to very hot conditions (hyperthermia) or become subnormal in very cold ones (hypothermia). Also, temperature fluctuates with a daily (circadian) rhythm. Typically, it is at it's lowest in the late evening through early morning, begins to rise just before dawn, continues to elevate until about noon, drops slightly for a couple of hours after noon, rises again until early evening, and then decreases again about an hour before customary bedtime. This is an evolutionary adaptation common to diurnal animals, and is designed to make the animal most active during daylight hours, with a small "post-lunch dip" (actually the technical term!) that encourages the animal to seek shade and rest during the hottest part of the day. (Many cultures incorporate a noontime siesta -- unfortunately, in the spirit of the true American work ethic, we buck our biology.) Anyway, temperature can vary by about a degree, more or less, throughout the day. If your son's normal temperature first thing in the morning is about 98.6 deg (considered average human temperature), then if you're taking his temp in the late morning or late afternoon, it could well be 99.6 deg or slightly higher. If he normally runs closer to 99 or 99.2 deg in the morning (still within the normal human range for body temp), then a late afternoon temp of ~100 deg is not far off the norm, for him.
Just curious -- if he's not showing signs of illness, why are you taking his temperature? If it's only to monitor him in preparation for immunization, you might not have noticed anything at all -- i.e., he's perfectly healthy. You are right, however, to make sure he's not ill before he receives vaccinations, but only because he will generate an additional immune response to the vaccine itself, which is likely to cause some elevation of temperature and may cause some localized swelling and pain at the injection site. If he's already sick, the vaccine may make him feel a little sicker, and why subject him to that? More importantly, though, is that some kids do have reactions to some vaccinations, and if he's already sick when he receives one, it could mask a negative reaction that should be reported to the doctor.
There's no reason to believe the vaccination will affect him negatively, though. The autism link to the MMR vaccine has been thoroughly dispelled since no one has ever been able to replicate Wakeland's studies, and his work has been fairly discredited at this point. Since thimerasol is no longer used as a preservative in American vaccines, the risks from mercury toxicity -- which can be associated with neurological injury -- no longer exist (unless he's eating a lot of fish, especially tuna and farmed salmon). Only a very small percentage of children react negatively to vaccination, and that probably has more to do with a genetic propensity of the immune system to over-respond in general than to vaccine components. The genetics of immune response is still a very young science, though, so there's no way to predict anything at this time.
If it helps any on a purely anecdotal basis, my daughter was also speech delayed and was fully vaccinated following the "normal" CDC recommended schedule. I can assure you there's been no affect to her intellect or speech abilities, which were fully resolved through speech therapy. She just graduated from high school with highest honors, was inducted into one state and one national honor society, is fairly fluent in French and is teaching herself Portuguese. I'm sure you'll hear from others who had negative experiences -- there's no denying that some children react very badly to vaccines and are, in all probability, vaccine damaged. However, by far the vast majority (over 97%, don't know the exact numbers of late) of children are completely unaffected, and some percentage of the 3% who are affected include kids who had only a mild adverse reaction.