There is a TINY hole in the bottom of the bore in line with the needle jet that sometimes gets plugged by water. Usually twice a year I disassemble my carb, including the stack in the float bowl that is held on with T20 security screws, and blow out all the passages. I agree it sounds like your jet assembly is put together a bit wrong. I think the main jet holder is supposed to hold the needle jet in place from the bottom.
The PWK Keihin is quite a good carb but like any of them, get one bit a little out of place and the bike will run but run lousy.