I'm not really crazy about this installation, but I'm not ready to say it's wrong.
1) Combustion air source: A garage is not a great place from which to draw combustion air. It is a location that can have combustible vapors from spilled fuel (from a sloppy refill of a lawnmower, a slow drip from a car fuel line, etc), which is why gas water heaters must generally be located some distance off the floor (18"?)-- to give at least a little margin if heavier fuel vapors are present, they at least need to fill the room for a bit before they reach the ignition source and explode. Also, garages can be more damp than the outside air (a wet car pulled in to the garage brings a lot of water with it). That moisture isn't good for the furnace, and bringing more moisture into the inside of the heat exchanger 24/7 year round will not improve its expected life.
There's already a PVC flue with a route to the outside, IMO not running a parallel PVC pipe for intake air is shortsighted when it could eliminate a fire risk and extend the life of the equipment.
2) Gas connection: The connection as shown is legal and common in a lot of places. Other places would require use of black iron and a drip leg/sediment trap between the gas shutoff and the appliance. If I were doing it, I'd put a sediment trap right at the furnace, required by local code or not. But, people differ on this, some think it is a waste of time.
2012 IFGC code: