Last Name Adjustements

As I'm sure you're already aware Brazilians and Brazilian authorities are absolutely obsessed with names and also with the correct spelling of them. It's so bad that even Brazilian must resort to applying to the courts to get simple errors in documents corrected, since the Cartórios here will not do that on their own; not even in cases where the error was made by one of the staff at the Cartório. They've got a whole bureaucracy surrounding the process of "Retificação de nome".

Given that, it's almost impossible to predict what is going to happen in your particular case when you apply for your RNE and Cédula de Identidade Estrangeiro through the Federal Police. I would suggest that YOU DON'T MAKE IT A BIGGER PROBLEM than it needs to be. If they insist on you staying with the old surname do it, if they find a way to resolve the problem without too much difficulty then that's great, but don't EXPECT that to happen. Absolutely nothing is simple here in Brazil, especially when dealing with the government in any way. Just go with whatever works for you!

Is correcting a marriage certificate is something which is doable according to the law? because if we fix that then everything should match 100%.

You would have to apply to the Courts in order to try and do that. I'm not sure if it is possible, only a lawyer can tell you for sure.

Understood, thanks for your help - following the above here is another question. When such problems occur that require process certain process, and I'm married & have a child with a Brazilian woman - and I am already registered as the father of that child - until all names related issues are resolved, will be able to get a work permit right?
They won't try to revoke my rights as a father until everything is resolved or any crazy scenario like that, correct?

If you or the child's mother registered the child in your name then you are legally the father. Otherwise if the child is only registered in the name of the mother you have no legal standing until such time as you go to the Cartório and do a process known as "Reconhecimento de paternidade".

You are only permitted to apply for your work permit, and other essential documents once you've actually applied for the VIPER Permanent Visa based either on having a Brazilian spouse or a Brazilian child, not before.

Keeping om this topic of change of surname: pur marriage was registered in my home country, where i kept my surname but have the option of adding my husband's. This is done by getting a new passport from home with all surnames strung together. I havent ordered this new passport yet but if i were to do it whilst my pedido de permanência still pending (where my name is registered as the unmarried one), what degree of havoc and confusion are we looking at?

Much more than you really want to find out.......... TRUST ME!