Water Pump Vs Timing Cover Conflict

Is it possible the timing cover just has some corrosion/ rust/ debri/ old gasket down one or the other holes?

So far as the timing marks you can create a pass. side one easy. Get yourself or just make a pointer. It does not matter exactly where the pointer points as long as you have a clear view down the pass side.

Now use a piston stop to create a new TDC using the new pointer. Then measure around the balancer with a thin flex tape, and figure out "degrees per inch" and mark the balancer out to 50* or so. I used to do this by jacking up the car some, then laying under and looking up at it. Way easier than trying to get "straight" view at it from above, or pulling balancer