IF alpacas are anything like llamas, they travel well!!
We brought our male llama at a year old, split him from his Mum and Dad and sisters (very sad for me to see him removed from his family!)
I removed the centre partition from our horse trailer, put some hay in, and in he went. We let him settle before leaving, and the owner assured me llamas will lie down to travel, and we peeped in and he had done, and stayed like that for the two hour journey.