Since the slow jet is fed via the main jet through a passage located above the main jet, the rubber plug must be there to avoid fuel bypassing the main jet and directly to the needle jet. If the plug is missing, the bike will run rich and there is no controle of the fuel delivery to the main system.
I would recommend that you buy the three next sizes of the secondary main jets, and then start with the largest. And the only way to find out if the mixture is correct, will be by riding the bike for 1/2 mile at full trottle on 3. gear, then pull in the clutch and stop the engine with the engine kill switch at the same time, stop the bike, and then check the spark plug colour. If it runs rich, you can go down on the jet size till you get the correct colour on the spark plugs. When the mixture is ok at full trottle, it's time to deal with any problem you might have in the mid range, or at idle.
It is also important that you adjust the fuel level in the float bowls to the correct level before you start tuning the carbs.
And you should also be aware that it is difficult to find parts for those carbs. Secondary main jets can be bought, but the primary main jets and the needle jets are hard to find. So in many ways, you will be better off by using the stock air box. And with the stock air box, and an aftermarket 2-2 or 2-1 exhaust system, most 400 owners have experianced that they don't have to rejet. But again, you can only find that out by testing.