Yes, on the 9.9 the fuel pump "pulse" comes through a channel in the carb.
There is three termination points on the bleed lines.
The bleed line that goes to the lower crank case connects to a check valve that should let oil/gas "out" (of the crankcase) into the line.
The bleed line that comes from the base of the carb scavenges leftover oil/fuel from the base of the reed cage. Likewise there is a check valve there that lets oil/gas "out" into the line.
Both the above lines connect to a T connector and the third bleed line takes the feed from both of those up to the top of the crank case to lube the upper main bearing/seal (upper crank).
If the check valves are shot you can end up with a an extremely "rich" situation which can appear as a flooded engine.
When you failed to re-hook the bottom line it should not have caused any fuel delivery issues. If the check valve was functioning properly it simply would have "misted" oil/gas into the lower cowl and you would get a slimy film similar to an "engine fog".
Likewise, the line that was normally connected there would have "dripped" goop that was scavenged from the reeds and your upper bearing would have got a limited amount of lube (the open hose would have been the "easy way out".
Now, if your motor won't start at all I'm fairly certain (without having the motor in front of me) that the bleed lines are not to blame, or certainly not solely to blame. Suspect that whatever the real issue is, is coincidental...