Sounds like it needs a new shifter cable, they stretch over time.
The clicking noise is the chain rubbing against the next gear on the cassette.
Get it serviced and it will be good again.
As for shoes, that's a big long subject.
I like flat peddles with angry studs and flat shoes. Lots of different brands and models. 5.10's were the best but sold out to Adidas .. RC is a new brand that some old 5.10 guys started. Good shoes so far for me.
Lots of people will say you should clip in.
That's not for me ..