B.Graham.
Are you sure the screws were timed, to start with( of course the one filed to fit the trigger guard was)? If they weren't, there is not much you can do, easily. If you are sure they were, the first thing to do is to be sure they are in the correct "hole". Those that either screw into or through the wood (stock, forearm)may be out of time due to wood shrinkage. A fix for these is to let a piece of wood into the stock, where the screw goes through, and work them down to where the screw is timed. A quick temporary fix is to put wood shims between the stock and tangs( this is also useful to see how much room has to be taken up. Where the screws go into metal parts, check to see if they have been marked to indicate whether they were intended for the right or left side of the receiver. A common way to mark the screws is by filing a line on the end of the screws intended for one side, and those for the other side are left blank. In cases where a third similar screw is used(drilling), the third one has a x filed on the end. The fix for these is to put them into the correct "holes". Where the shrinkage is very severe, the tangs might be pulled so close together, the gun won't function. In this case, shims or additional wood would be needed, anyway. If the stock has been refinished, and oversanded to the point that the metal "stood proud", the tangs might have been let into the stock deeper, causing the problem. Of course, since I haven't seen the gun, this is only speculation.
Mike
