The EdgeRouter Lite only has a 500MHz dual core MIPS CPU. They are most likely only capable of reaching gigabit speeds when using the stock firmware from Ubiquiti, enabling whatever form of acceleration they have (hardware / special kernel modules / ...).
For comparison:
A Zyxel ZyWALL USG 60 has a 400MHz dual core MIPS CPU which hits around 70% usage on a 120Mbit connection with only the firewall active and all other UTM features off using their stock firmware. AFAIK Zyxel has no form of hardware or software acceleration in place at the moment.
So if you want to get the advertised gigabit speed from the EdgeRouter, you either have to use the stock firmware or wait until OpenWRT/LEDE can utilize the same form of acceleration Ubiquiti can.
IIRC a friend of mine also told me the performance of the EdgeRouter was impacted (even on the stock firmware) when he enabled bridging as that happens in software and affects the CPU. Maybe it also disabled acceleration.
Just a question:
Why do you want to replace the Ubiquiti firmware? It's not your usual home router crap and gets updated quite often.