Unless somethings changed in newer releases I think you will need to modify all the required pages in the custom page zip (check the reference guide to work out which ones you need to change).
Having said this it is fairly straightforward to give the pages the same look as a standard page. The template files use parameters for the various text which can easily be set at the top of the file. For example to set the Portal name just add the following near the top of the file (I put them before the <html> tag)
<% SET portal = 'Your text' %>
Most of the parameters have a similar name to that on the standard page config so with a little searching you can work them out and their all documented in the CSP guide.
Once you've set them for one page you can just copy and paste them into the others.
You then just need to tweak the logo and background colour.
Of course what would be really cool would be if in a future release Juniper set it up so you could set the parameters on the in the Custom Sign In page config on the box or even tell it to use the values from a standard sign in page. This would make small changes to the sign in pages like you want to do a lot easier.
