Yeh you are always better keeping it cordial, just explain to them your thoughts and see what they have to say...
Brakes/Horn - This could have happened afterward. Get them to have a look, if they are reputable then they will own up and sort it or explain why it couldn't have happened on their watch.....
Scratch - If it happened in their care then yep they should sort it, although proving it is another matter.
Engine rebuild - It all depends on what was agreed in the first place. Engine rebuild is a massively open ended term and could include lots or few components. Spark plugs/Air filter would be replaced as part of a service rather than a rebuild although it makes sense to change them. Fuel filter has nothing to do with an engine rebuild and the Dizzy wouldn't be replaced. As long as you didn't pay for these bits then you have not been diddled.
With regards to the invoice most places invoice monthly although i have had them 6 months after the work was done. I'm not sure if there is a legal time frame they are supposed to supply you with one in.
Sounds like more a case of the garage not knowing what you were expecting and you not knowing what to expect. I wouldn't get angry just talk to the people and get it sorted.
