2004 F115 TLRC Runs rough in gear and idle

[Majek RFL]

I have a 2004 Yamaha F115 TLRC with approx. 700 hrs that I bought last summer, It purrs at idle, purrs under power, but runs rough like it drops a cylinder or two when I put it in gear at idle. I have swapped plugs, injectors, and coils/wires and it doesn’t seem to change. I also replaced the ISC valve.
Anyone else have this issue?
It started doing this after I changed all of the fuel lines, filters, pickup tube, cleaned vst and replaced both fuel pumps. Fuel pressure is approx. 40psi.

 

[Majek RFL]

I believe I have fixed this issue. It appears the engine needed to be synced... Headed out to do a sea trial, but it appears to be fixed in the driveway, and I can reproduce it by unsyncing the screw.