Hi, backyard;
You're being introduced to the world of the 1946 Holley. It can be a bugger until you understand it: by practice over the last 8 years, I've become an expert on this one device!
First of all, the overflow you're seeing is caused by the hot soak. The fuel lines heat up after engine shutoff and the fuel pushes past the float valve and into the fuel bowl, overflowing into the engine. However, the reason it did not bother you before the rebuild is because you have inadvertently set the float level a bit too high. Given the way the rebuild kit told you to do it, it's extremely easy to do. Here's the kicker: you MUST get another rebuild kit before you go in and readjust that float, because as soon as you open the top of the carb, it will ruin the seal around the vacuum port that closes the power valve. If, in fact, you assembled and disassembled it once (or more times) with the existing gasket, it already leaks, which makes the hot soak situation even worse.
So, here's what to do:
1.) Go get another rebuild kit. The cheap ones from Checker will do just fine ($9, I think). You will need that large 'top' gasket.
2.) When setting the float, go to the next LOWER setting you see in the chart that comes with the kit. I think I used the California setting on mine last time. Since the 1946 runs rich to begin with, this will make the engine smoother, anyway, and won't hurt the engine one bit. It gives the float bowl some extra room to hold the fuel that comes in when the fuel line gets hot after engine shutoff.
3.) If you are looking for better gas mileage, cut 1/2 turn off of the spring that holds the power valve open: most kits give you a new one, anyway. If you have 2 springs available, select the one that's weakest. If they are the same, cut that 1/2 coil off of one and use it. This will let the power valve open slightly later. Since the intake log does not respond quickly to large throttle changes, you probably won't notice any difference in acceleration: I have tried it with 1/2 and 1 turn cut off and noticed no acceleration differences, but got 1/2 MPG for my trouble (in-town driving).
4.) This is VERY important: most of the time, the cover's screws are stripped on these carbs. If yours are, ESPECIALLY the CENTER ONE, then go to a hardware store and get a #12-24 tap and screws, about 1-1/8" long. Drill and tap the stripped ones up to #12-24. Reason: if the center screw or any of the 3 across the carb in that plane are stripped, the power valve WILL leak fuel all the time.
Check this, too: open the hot-air line from the exhaust manifold where it plugs into the choke housing. Run the engine and see if exhaust gases are coming out of the little pipe. If it is, then the tube inside the exhaust manifold is corroded away and this has been overheating your carb. If you're lucky, it has not warped the top plate of the carb (if it has, you need a new carb, period). If the carb is OK, then make a new choke heater by wrapping 6 turns of 1/4" copper pipe (like from a refrigerator's icemaker water line) around the exhaust manifold where it joins the exhaust pipe. Connect one end to the choke, like it was before, and connect the other end to the nipple that comes out of the passenger's side of the carb's air horn, at the top. This is where cool air enters this heater system. It gets pulled along by the manifold vacuum that is ported into the choke housing, and is required to make the electric choke function properly. (See my other posts about the 1946 carb. Some are in the Hard-Core Tech section).
Drop me a PM if you need more help.