I haven't done a 4040 r/o housing but Vin has.
The Ro/Man type r/o's where easier as you just fill a plastic bucket up with a very strong concentration of bleach and water and put the empty housings and screw caps in along with the 1/4" piping.
With the housing of the 4040 being bigger, I would remove the membrane, put the end cap back, leave the inlet hose and pure hoses connected, stand the housing upright and carefully pour a strong mixture of bleach mixed with water into the pure outlet hose with a small funnel until full. Open the waste gate valve for a moment to get the connectors treated, close up and leave for a few hours. Empty the contents of the r/o into a bucket .Then thoroughly rinse the housing with water. I would then suggest that you treat your carbon prefilter the same way using the bleach mixture from your bucket, and then put the inlet hose, pure and waste hoses in as well.
Our r/o has always gone through the di vessel before going into the tank. If yours is the same as mine, then I would also bleach out the di vessel (empty) and hoses. Whilst you are at it, I would also fill the IBC tank to the to top after putting bleach into that, leave it overnight, drain using your sub pump and thoroughly rinse out.
I would also use the opportunity to bleach the van tank as well. Fill that with a bottle of thick bleach, fill it up with tap water, drive around a bit to get it sloshing about and leave overnight. Drain and thoroughly rinse out. If you have a pressure washer, all the better.
Getting the last bit of rubbish from the bottom of the tank isn't easy so be prepared to clean your pump filter out every few days.
Treat this as a hospital deep clean.