Thanks all for you help
A little more information and maybe a little more advice required.
Since fixing the malware http://domain.com/index.php?vc=201&Cheap_Adobe_Acrobat_xi and similar are actually no longer pages. Joomla actually sees anything after ? as a parameter and just ignores it because it no longer matches a page and hence the reason it just defaults to the home page http://domain.com/index.php. This is Joomla and probably most other content management systems default behavior. The problem here lies in the fact that google indexed that page when it was infected and it remains in the index because to google it sees a status code of 200 when re-indexing this page.
The problem is now a bit broader and has more ramifications than first thought. Any pages from the previous system that used parameters would receive a 200 status code and remain in the index. Checking url parameters in web master tools confirms this with various paramaters showing thousands of url's monitored. Keep in mind google is showing a message that there are no problems with parameters for this site.
So the advice I need now is related to url parameters in Web Master tools. The new site uses SEF URLS and so makes much less use of paramaters. How can I ensure that the old redundant pages with parameters are dropped from the index. This would involve thousands of 301's or 404's let alone trying to work them all out. There is a reset link for each parameter in webmaster tools but not much documentation as to what it does. If I reset all the parameters would that clean up the index?
I'd be interested in what others think about this issue because I feel that this might be a common problem with cms based platforms and after major changes, thousands of paramater based url's just defaulting to home and other pages probably affects the site and page ranking.
Ian