I would hold off on the manifold. The EX and EX-R have the same motor and manifold but 10 HP difference. Based on the article below its due to the ECU programming. I would put $ money into the ECU reflash before a new manifold, gaskets and labor (who knows if it even will fit or route properly in the SJ4 engine bay)
from boats.com:
The WaveRunner EXR ($9,299) is more powerful and lighter in weight than standard
EX models, a formula intended to boost acceleration and top-speed performance. To increase power, Yamaha dropped the three-cylinder, 1,049cc
TR-1 HO engine into the EX hull. This high-output version of the TR-1 makes about 10 percent more power than the standard TR-1 engine, according to Yamaha – a bump to approximately 110 horsepower from 101 horsepower (Yamaha does not publish horsepower figures). Yamaha says the power gain is accomplished in the engine control unit (ECU), which is programmed permit 8000 rpm in the HO engine, compared to 7300 rpm in the standard TR-1. To take full advantage of the added power the EXR is also fitted with a new top-loader intake grate that better feeds water to the impeller and a 40mm jet pump extension that increases acceleration response. With a single rider the EXR will offer a top speed of about 54 MPH, compared to about 50 MPH for the WaveRunner EX Deluxe.