I just tried upgrading from Atahualpa 3.2 to 3.4.2

I cannot get the logo, header and ico I had installed on my previous version to show though even though the settings do not seem to have changed.

For the header, I went into into Atahualpa342/images/header and deleted all the other images apart from the one I wanted. However, I still get the Atahualpa default header I do not want!!

I tried looking at the page on a different computer but still have the same problem.

You should really upgrade to 3.5.3 using the manual method as outlined in the FAQ thread. That version is old enough that I wouldn't know how to accurately help you.