I can find no direct reference to those nozzles on your new carbs (for jet skis)....however, while looking through the Mikuni carb catalog I noticed similar nozzles on snowmobile carbs.....on SM carbs, those nozzles are referred to as "Power Jets".....the catalog goes on to say...."Power Jet kits are used in 2-stroke engine applications to improve mid-range throttle response and add additional fuel to WOT running conditions".....so it makes sense what MoDawg73 said...."accelerator pump nozzles"....IF YOU HAVE accelerator pumps....IF not, then seal them off with rubber caps.
And a little notice in your pictures.....the linkage bar for the dual throttle setup typically has the little tick marks on the main adjuster and the nut on the PTO side of the assembly....I noticed your old setup was correct but the new setup was reversed. Supposedly, the tick marks go on the PTO side so if you had to make in field adjustments on the link bar, you could actually see them easier if the ticks are on the PTO side.
PS...You are changing out all the old grey Tempo fuel lines too, I assume?