Question: The carburetor kit has two check balls. Where do they go?

Two check balls come in the kit, but only one is typically used. It is the ball in the power valve which gets replaced, and it is best removed by inserting a punch or other pin through the holes in the valve body while unscrewing the jet from the bottom. IMPORTANT: a tiny spring goes in between the jet and the ball; don’t lose it upon disassembly!
The other two balls in those jets/check valves in the bottom of the bowl are captive and cannot be removed from the assembly. They must, however, be loose or (at the very least) the accel pump won’t work. And it is still a good idea to remove those valve assemblies to clean them and beneath them — if they will come out.
I asked Jeff about making a push up rod for the Carter updraft BB-1. They are not available anymore and the though was that perhaps we could make it ourselves.Here is his answer.
Sorry, no, I don’t have the spec on that rod. The diameter is either 3/32″ or 1/8″ IIRC, and it should be tapered somewhat on the end which goes into the power valve in the bowl bottom.
To determine the right length, take a piece of brass rod and push it down into the power valve to compress the check ball spring. With the spring compressed, mark the rod at the exact point where it is level with the top of the bowl casting gasket surface. Now invert the bowl lid and place the rod into the vacuum piston hole but DO NOT COMPRESS THE PISTON. Mark the exact length from the piston to the bowl lid gasket surface. Measure the two marks on the rod and add the two figures plus 1/32″ for the gasket thickness and you should have the length to which to cut the rod.