My 04 TR21 was originally rigged with a merc. I bought it and had a 08 250 HPDI installed. They used a new pigtail for the boat-side harness to attach to the Yamaha motor. Cut and spliced to the Merc harness.

So the boat still has the Merc Commander 4000 shifter.

I have changed all the switches on the motor's shift linkage. I still experience stalling once in a while when I shift from fwd to N or R to N, sorta thing.
I was thinking of replacing the neutral switch in the Merc shifter but that is nearly impossible to get at!

Also, from looking at some wiring diagrams of the Yamaha motor side big plug, I don't see anything related to a neutral switch at the shifter.

Can someone fill me in on how this all works? The conversion from Merc to Yammy, etc...

Thanks