The EEA2 Application fee is £55 as you have mentioned. There is nothing else to pay, though you will probably want to send, and have your documents returned to you by Royal Mail special delivery, which will cost you around £10 more.
You may be interested to know that my non EAA step-daughter applied on 22 August 2013 and it is not yet issued, even though hers is a straight forward case. In fact, she did get an acknowledgement letter after a few days advising she should not try to contact them unless she wanted to get her passport back for an emergency(in which case the application is cancelled!)A few days later she received another letter saying it was a 'Certificate' to say that her application was at the Border Agency. It also advised potential employers that she could work until six months after her application date only, unless she could produce her residence certificate. Also said employers should first check status with Border Agency, which makes their 'Certificate' useless.
Another point. Under EU law, the UK is required to action all EEA2 applications within 6 months , but not long ago it was fined by the EU for failure to comply. A recent press report claimed that over 60% of all applications to the Border Agency are either not actioned at all or are overdue. So don't expect anything back in a hurry.