"Fuel pump has one inlet and two outlets" - got it.

"One outlet goes to the float bowl" - got it, I hooked up the fuel hose that looked like it went to the Mikuni fuel bowl to the only fuel inlet fitting on the Weber.

"The second outlet (regulator bypass) goes to the accel pump well, and then to the tank fuel return line" - well, since there isn't an "accel pump well" fitting on this Weber, and you say it goes to the fuel tank return line, and there is that third hose from the Mikuni that goes back to the tank, then by default these two hoses should be connected, or replaced with one long hose that goes from that second outlet on the fuel pump to the fuel tank return line.

That's what I'm reading from your post, so if it's wrong, let me know. I may be a little slow on the uptake sometimes, but I'll eventually get it...