OK everybody, good news
We went to the offices around the back of the immigration today (which Mark recommended, thanks mate), we walked up a hill and at the top is a large 2 storey office building that is the customs offices, open Monday - Friday only.
In the front door and straight up the stairs there is a nice big sign and top of the list is Tiempo de Tramite!
10 mins later we had the temporary import document (he wanted to see ownership papers and IDP and passport).
I would recommend if you cross at Ciudad Del Este just going into imigration to get your passport stamped then ride away from the office, take the FIRST right following the building round and ride up the hill behind the office you have just been in, park up outside (security everywhere) and you'll be sorted straightaway.
Don't even think about trying to get your Tempo docs at the actual crossing point, the main guy's is a fool and unwilling to help, he is quite happy for you to ride off into Paraguay without the correct paperwork and suffer the consequences, nice attitude from an offical!