Thanks for your feedback esmi and perdur..
For future readers…
To resolve this I was able to assign a PHP widgets to the section of the site i was trying to rectify. This was done through the admin panel -> Appearance -> Widgets
I retrieved the code for the banner ad from the OIO Publisher plugin and the search function was a default widget that I simply dragged in to the ‘middle footer’ menu bar on the right hand side of the widget screen.
To scan and remove the Malware I used the Sururi software which defected and cleaned the site within 3 hours. immediately after this I received an email from google saying the site was clean.
Thankyou, this issue (to me anyway) appeared difficult to fix at first and was actually very easy and fast thanks to the help of this forums users..
