You do want a check valve in the RO membrane permeate port or if not in the port then in the tubing just downstream. Is the check valve stuck closed?
When permeate (RO water) production drops the most common cause is that clogged prefilters (all the filters that touch the water before it reaches the RO membrane) are clogged and stealing pressure from the membrane.
Are your prefilters clogged?
Do you have a pressure gauge on your system? What does it read? Is the gauge installed to read pressure after the prefilters but before the membrane?
Pressure tanks also go bad. If you open the faucet and get about a half galss at normal pressure and then just a drible, it may be that the bladder in the tank is bad. This is not uncommon. Solution is to replace the tank.
We'd need to see a picture of your RO membrane housing to be sure, but chances are you could just replace your membrane with an industry standard TW1812-50. Your 400 ml/min flow restrictor is ok to use with a 60 gpd or a 50 gpd membrane.
Buckeye Field Supply