1) Replace them all - but if you are taking it to be set up, they'll do that as a matter of course.
2) Matter of taste, but I like Fender or D'Addario phosphor-bronze for acoustics.
3) Again, it's a matter of personal preference, but I would go for 11-52
4) Not a lot - until you've practised a bit, you'll have sore finger tips, regardless of the gauge.
5) They'll check the straightness of the neck, look for any high or low spots on the frets, check the condition and height of the nut and bridge saddle. What they actually do will depend on what they find when they check it.
There's not much room for adjustment of the action on the F130. Acoustics sound better with a slightly higher action than electrics. Yamahas tend to have a decent action out of the box.