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Those pipes hang quite a bit lower than TZ pipes of the era that fairing was designed for. Typically Yamaha tucked the pipes up tight under the motor/frame for maximum lean angle. That fairing has the H-L powervalve shaped top half with the lower part cut higher - like a C-D-E aftermarket shape. It's an interesting aftermarket design.
Fortunately there's enough material that it can be trimmed to clear the pipes and to get more leg/knee clearance.