It will might others users if you post here step by step what have you done wrong/right. Keep it simple as possible. Sometimes topics get too long and dispersive if we can recapitulate everything would be awesome. It will also help the dev team.

Step 1.

Delete all your phpnuke folders from your /public.html directory, or whichever folder on your server phpnuke is installed into.

Step 2.

Upload all cpgnuke folders to your public_html directory, or whichever folder you are using on your server.

At this point make sure ALL folders have been uploaded correctly, i found that i had to upload them one by one as my FTP client kept timing out.

Upload the mainfile.php and the modules.php files from the Documents/phpnuke folder of the package of cpgnuke.

step 3.

Run the installer. I.E www.yoursite.com/install.php.

Dont forget to change the table prefix to whatever it currently is, otherwise you will get a fresh install instead of an upgrade, it should be nuke_ as default for phpnuke.

At this point you may encounter an error to do with the nuke_bbusers table. Take a backup of the table using phpmyadmin to your harddrive, then drop the table nuke_bb users, then run the installer again.

Step 4.

Once the installer is finished you should be able to login to your site. If you have any problems, for example your users are missing or your forums have no content, just copy over the relevent tables from your old phpnuke database to your new database, as i found that the installer updated the nuke_bb tables but it did not keep any of the content of them.

I found the easiest way to upgrade was to not do it with your "Live" site, as so many things go wrong.
The best way to do it i found, if you have the server space available, is to create a sub folder and a new database, and copy over your phpnuke database to the new one, and upload the cpgnuke files to the subfolder and work with that, then once it is all up and running all you have to do is copy the upgraded site files to the root of your server.

I now have another problem !!

When the site was running phpnuke, all the signatures were working, now i have converted they are not.

Is this because phpnuke uses html for signatures and cpgnuke uses bb code? or am i completely off of the beaten track?

If i am correct, is there a way to change them en-masse if you like?