Not having the wings on or the elevator cables tension should not make a difference in my opinion. I too have the upgraded pump. Once again, The length of the push rods, including the flap handle push rod are crucial. I'd remove them and measure them precisely. I assume that the interference occurs with the flap handle set in a detent (?) ... check it in all three positions.
The geometry is very subtle. But the length of the rods causes the two main flaperon push rods to sit higher or lower just slightly. That was my problem anyway. My flap handle pushrod was longer by an 1/8 of an inch and my flaperon push rods were also of just slightly. When I corrected these, the fuel pump interference problem went away.
White Salmon, WA
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