Is there a way I can set a clearance on individual pads of components. I need to make sure certain points do not have other components close to them and want errors to flag up if I make a mistake somewhere.
Don't think you can specify individual pads but you can specify individual nets that may be connected to the pads. The net match feature is extremely powerful, I have now done a few multilayer boards requiring different clearancies on different layers for the sam nets.
You could redefine the component shape so the pads have for example a silk screen shape around it. If you do not want the shape visible on the silk or you need the shape on the pad then the shape could be defined on another layer, according to the help file placement needs to be set in layer type to be yes.