1) In the shop manual, they say turn the harmonic balancer (crank pulley) top dead center. Which cylinder is supposed be top dead center?

2) What is the best way to know if that cylinder is top dead center?

 

Cylinder 1 (or 4 honestly, they move together)

The "front" of the engine is typically where cylinder 1 is, that's the side that is furthest from the transmission and closest to the serp. belt. In K20 cars, that would be the (USDM) passenger side of the car. take the valve cover off and spark plug out from cylinder 1. Rotate the pulley until you see the camshaft gear markslining up with each other (there will be small nothches on intake and exhaust, 2 will point towards each other, I'm sure your guide goes into this.) then stick a pole, long screw driver, or other lengthy rod-object slowly into the spark plug hole of cylinder 1. I use a small parts grabbing tool thingy. It's now resting on top of your #1 piston. Rotate the crank pulley until that rod, and the piston, is at it's highest point. The cam gears should line up (or be close to it, if they aren't your engine is not in time.) If the cam gears aren't anywhere near lined up, you're probably at TCD exhaust stroke. Spin the crank another rotation.

 

hopefully this helps. #1 can also be TDC of exhaust stroke, you want TDC of compression stroke. Look for those cam gear marks to line up.