If you put a pump on an outboard you lose 30% of your horsepower, and I don't know if anybody makes a pump for a 15 Yamahammer. The smallest motor I've ever seen with a pump was a 25hp Merc.
On my Merc the zinc anode has a fin (or skeg) that can angle either direction to compensate for the rotation of the prop and motor. It just has a bolt thru the middle that loosens it so it can be set where you want it. Yamaha might be similar, but I've never looked at one. They have to have some means of adjusting for torque steer.
This alignment thing sounds kinda weird. If it was serious, you'd have major problems like water in the lower unit and exhaust/oil leaks. It depends on if the alignment is off laterally or vertically. Hard to tell from here.