It just taken me a couple of hours to find out how to change the FastCGI timeout settings on IIS 7 for PHP so I thought I'd post the info here for anyone who may need it.
Its really simple in the end, just download and install the IIS7 Administration Pack:
32Bit: Administration Pack for IIS 7.0 CTP2 (x86) : Download : The Official Microsoft IIS Site
64Bit: Administration Pack for IIS 7.0 CTP2 (x64) : Download : The Official Microsoft IIS Site
Install on your IIS server, open IIS Manager and select the server. Under IIS you will now have an extra option of FastCGI Settings.
The main two settings in here that may cause problems on slower servers are the 'Activity Timeout' and 'Request Timeout'.