Your concerns are definitely valid. In fact, I believe that any concerns a parent has about their child's well-being is valid :) When it comes to the link between vaccinations and autism unfortunately the jury is still out. There are many out there that will say that the link has been dis-proven, but there are new studies that have come out just this year that once again suggest that there may be a link.
The newer studies are now suggesting that the link is NOT restricted just to the MMR vaccine. It is known (and recognised by both government bodies and vaccine companies) that vaccines can result in encephalopathy, and that encephalopathy can result in autism. The Vaccine Injury Compensation Program in the US has even compensated some parents who believe that their child has become autistic after suffering vaccine-induced encephalopathy.
Whilst most children will suffer no brain damage from vaccines (brain damage is estimated at 1 in 1 million after the MMR vaccine), some people have a mitochondrial dysfunction that can develop into autism after vaccination. Some people will never know they have such a dysfunction, but it can run in families, so someone in a situation might myself who has two brother on the autistic spectrum and a husband with a son on the autistic spectrum, might be more likely to have children with the dysfunction if that is what the other family members also have. It's for that reason that we have not vaccinated at this point in time on recommendation from a specialist.
The current President of Merck’s Vaccines Division, Julie Gerberding, confirmed to CBS News when she was Director of the US Centres for Disease Control that:
"if you’re predisposed with the mitochondrial disorder, it can certainly set off some damage. Some of the symptoms can be symptoms that have characteristics of autism.“
If you decide to give the MMR vaccine I would suggest making sure you DO NOT give panadol before or after the vaccine. Although many health professionals suggest giving it, a 2008 preliminary study found that paracetamol use after measles-mumps-rubella vaccination was associated with autistic disorder. Ibuprofen was fine though.
Knowing that your child had some form of reaction to his first vaccines is very good reason to have concerns about future vaccines, so regardless of what you decide to do, don't let anyone feel bad about your choice :)
Just a little bit of a disclaimer: Anything I write is either personal opinion or based on scientific peer reviewed studies. I studied microbiology at Universary and have a Bachelor of Science with first class honours. I only write this because I know there is a lot of information and "facts" on the internet both for and against vaccination and I wanted to ensure you that I don't get caught up in all the non-scientific hype :) At my last visit to the GP my doctor actually laughed and said he was glad I had a science degree because it made him comfortable that I was fully informed. He then admitted that whilst he is pro-vaccination, that all the information he gets is from the vaccine companies and that I probably know more about vaccines than him, lol. It's nice to have a GP that is supportive rather than condescending :)
EDIT: Also, I have a number of journal articles on the subject so if you would like any of them please pm me :) Some are rather loooooooong haha