Could it be that this trojan is adding codes such as 'eval' or 'ef56' and by that causing errors for my forum?
It's most likely because of that. You need to determine the nature of the error... how it could be possible? Do you use other 3rd party scripts on your website?
How can I change that back again? It wasn't my intention to do so. I'm not an expert so I've probably changed something without knowing.
The copyright link is untouched under the original main_footer.html template, you can just put it back... Anyway who will believe you that it was done without knowing
:-) You absolutely knew what you're doing replacing copyright URL and the original image, thus modifying the core index file...