Are you source files from IsoDraw or they strictly CGM? By the sounds of it, CGM.
If this is the case, try opening one directly into IsoDraw and see where you sit. If you're lucky you might be able to do the following.
You likely could just set the desired frame size (assuming they are all the same) in the default settings of IsoDraw. To do this, close everything in IsoDraw and then change the frame size under preferences. This way, when you open the CGM it will be placed on that frame.
If the frame varies, you'll need a way to determine the size of the original frame (naming convention maybe or a bounding box).
My guess is that no matter what you will run into a placement issue...meaning that the CGMs won't be placed where you want on the frame. By opening the file with the desired frame size already set you can see how that comes out. Seems like we had problems with that, but it's been a few years since we migrated and thus had to cover this issue.
If placement is an issue you check search the forum for a macro that centers the contents of a file. So what you could do is use the batch tool to convert the CGM v3 to CGM v4 while using the centering macro.