You say there is no fuel in the filter. I am assuming that you are using a clear plastic filter with a paper element. Remove it. Install either a small disc fuel screen filter, or a steel housing fuel filter. Those cheap plastic ones for some reason tend to inhibit the fuel pumps ability to suck. I don't know why. Even if it is the same style that was original, remove it. I suggest using a disc/screen style to see if the problem goes away. If so, then move up to the steel housing filter and see if the issue returns or not. Pretty sure the issue is the filter style. I've seen this before.
On a second note, I don't see where you replaced the fuel pump. Your pump may also be weak. I suggest going to an electric pump mounted near the tank.
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