Those plugs are necessary. Fuel is fed though the main jet and then over to the pilot jet. Not sure why Mikuni designed the carbs that way but it's fact.
Regarding the O-ring, that looks like the wrong one.
It will run too rich and foul the spark plugs without the plugs installed, I have found some o-rings and rubber plugs swell to double there normal size in gasoline.
It seems you got a mixed set, 3 made of material that doesn't swell, and one that does. If you let it dry out for a day, it will shrink back down.
Regarding the pilot jet plugs; some carbs need them, others don't, and you can tell by looking down the bores of the jets. If there's a hole in the side of the pilot jet's bore, then you need plugs. If it's just a straight tube, no plugs. If yours has them, you probably need them!
Regarding the Harbor Freight O-ring kits - I've found mine to be very useful to have around, but now and then there's a specific diameter or thickness of ring that isn't included; so it's a good set to have, but keep in mind that OEM may be "ideal" for some situations.
Yes! I found a small pack of O-Rings at an auto parts store for $4 and it had one 0-ring that was just right. Plug slid right in.
Didn't think of that, but it was an easy solution. I know it won't be as good as a OEM O-ring but I think that O-ring was from a rebuild kit anyway.