Sounds like it could do with a service!
What makes you think the handlebars are upside down? Those are thumb shifters and not downtube shifters, they are meant to be like that and the set you've got looks like a half-decent pair!
Also, the 'spare wheel clamp' is meant to be there! It's a quick release for changing the height of the saddle when offroading, most riders would lower the seat before a technical downhill section!