Assuming that the bike is rideable, I would check to see if it passes the hands-off test, i.e. whether it has any consistent tendency to pull to one side when you ride. That can tell you a lot about whether the frame and fork are straight and properly aligned. As a teenager I once bought a road bike that looked pristine to my eyes, but had a bent fork.

As for the shoe/pedal issue, Performance usually has cheap pedal/shoe combo deals - there's one on now for $70. If you get the $100 bike and $70 pedals and shoes, you still have $30 left over for some titanium chainring bolts ;-)