I think your bike shop is poo, and they're gouging you.

For example, the cog on your freewheel shouldn't have been replaced; one of these should last years and any rust on it is purely cosmetic. Almost certainly wouldn't have been a rubbish cheese one on 1k Euro bike.

And a new wheel with broken spokes that isn't fixed free of charge? That's the mark of a crap shop. They don't understand it's their responsibility to ensure wheels have adequate tension when the bike's sold.