As far as what you are describing with the flower pot not getting fuel/water from around, if I understand correctly, this is covered in the Tech Manual. There is a square hole which the fuel return line runs through to get into the flower pot. Of course the line is round, so the clearance between the round line and the square hole provides a path for the fuel to "equalize" to the inside of the flower pot as fuel is used from the inside of the flower pot. This can be cleared with a hanger (I believe, as I didn't need to do this). But, if there is lot of gunk in your tank, it could block the flow again.
Prior to removing the tank, how much fuel was in it (approximately) when you were having your hot running issues?
If it was above the top of the flower pot, you have more things to be concerned about, because if the fuel level was that high, it had a clear path to the screen without having to go through the square hole .... either way, the fuel does need to get through that square hole.
I hope this helps.
Mark