fuel pressure dropping over time

Your return line might be your issue. It should ALWAYS be as large or larger than the feed line. Stated on p. 2 of the 4309 instruction sheet.
I also use the 4309 reg, bypass mode, with an elec pump. I use a 3/8" feed line, 1/2" return line. Rock steady fuel pressure.
A bypass system is basically a 'full circle' system. Beginning at the tank & ending at the tank. The engine [ via the regulator port ] takes what fuel it needs.