So, wait. If you connect the fuel line to the pump and bottle with the fuel line not reattached to the stove, it works, but if you reattach the fuel line, it stops working? That’s weird. Really weird.
Maybe something gets dislodged during the process of reattaching the fuel line and hose to the stove?
I’d probably disassemble the thing again and go through it part by part. You should be able to blow with your mouth on the end that attaches to the pump and hear air coming out the jet. You should also be able to hook it up to a dry bottle and hear air coming out of the jet.
If you’re already hearing air, and this is going to sound dumb, but make sure you’ve put the pump in correctly. You probably have, but you need to make sure that the fuel pick up points down and the air supply tube is oriented up. The fuel pick up is closest to the pump handle, and the air supply is the furthest from the pump handle.
Click to enlarge

This is an older pump, but with in the bottle, as the bottle lays on the ground, you must have the tubes oriented as shown. On the newest pumps, the air supply is a hard plastic instead of a little tube. Still, though, it must be oriented up when the bottle lies on the ground. You laugh, but sometimes we get so focused looking for a technical problem that we overlook something basic.
If the orientation is correct, make sure the fuel pick up angles well away from the body of the pump. If the fuel pick up is pushed in toward the body of the pump, then it may not pick up fuel correctly. The most recent pumps have a white filter on the end of the fuel pick up.
Edit: Bob’s idea is good. If the cable is too far into the line, it might push the shaker jet into such a position that the shaker might seal the jet. Make sure you can hear the shaker moving in the jet when you shake the stove.
HJ
Adventures in Stoving