Jake,
The pump could be causing a restriction. I would remove it, hook a hose to it and see how it flows with a fuel source (could use a funnel) about 2 feet above the pump. It should flow like a weak urine stream. Also check that the hose connections are tight, to make sure your system isn't sucking air.
The check valve in the pump could be restricting flow, so could the flow transducer and the filter (if its dirty). Have you checked the flow out of the pump (right before the engine pump) with it on and a hose running into a container? it should be a much stronger stream. Also check the voltage at the pump while it is running, it should be over 11 volts. A bad ground can also cause a weak pump, but that won't show up during the voltage check. Voltage/ground problems can be due to bad connections or undersize wiring.
Is the vacuum line that powers your pump tight and in good shape?
What was your max RPM before you installed the facet pump? Did you change anything else?
Do you have EGT monitoring on your cylinders? Do they go high right before you go full throttle or at full throttle?
Ideally I think you would want the facet pump mounted below the fuel source so its gravity fed. Autogas can vaporize when a vacuum is applied at high ambient temperatures. With the engine running, tied down and at 3500 rpm (be careful by the prop) do you see any bubbles going through the filter (if its clear) you shouldn't. That means its vaporizing from high vacuum due to restriction or sucking air somewhere before the filter. Do you use Tygothane clear fuel lines? That also makes it easier to spot bubbles.
I prefer to have a filter mounted after the facet pump, since I have found small particles given off by the pump due to wear.
Those plastic clear filters can have a ridge on the barbs from the molding process that can allow air to be sucked in. If it does, use a knife blade and scrape the ridge down to where it is smooth with the rest of the barb.
If all this checks out I would take the engine mounted pump apart to check for blockage. Be careful with the diaphragm and don't use any chemicals on it. Also check the flow through the transducer, you should be able to blow through it easily. I would also check the carb bowls for debris. A new facet pump may have released something that is restricting your flow downstream.
Be very careful about running your engine lean due to a fuel problem. 2 Cycles will not tolerate a lean and hot burn.
Kevin K.
Sonex Jabiru 3300