So I picked up a boat that has an 01 Yamaha EFI 225.

The plugs that are currently in it are BR9SH10 instead of BR8SH10 both NGK's. The manual says BR8SH10, so why would there be BR9's in there instead? The boat hauls [censored]. its a Skeeter ZX225, and has 27p prop. I hit 74 already with more to go, but the motor smokes alot and idles rough so I was gonna do a tune up. Should I put BR9's back in?

no. Put the 8's back in. The 9's are too hot and would only be good to do a lot...LOT....of trolling. If the engine was loading up and the mechanic didn't know what to do, he problably put in the 9"s.

You need to have the manual fuel pump diaphrams changed and do as Mike said.

I changed the fuel pump assemblys out already. The cowling says BR9's so thats what I put in there. I also decarbed engine. It idles good now, still smokes a little when idling but not to bad.