I'd start by disconnecting each stage and then turning on the water for a bit. Once the water from the first stage runs clear, turn off the water, hook it to the next stage, flush the next stage, etc. until you've flushed all of the stages before the RO membrane. Once you get the RO membrane hooked up, throw out the first few gallons you get from it. I don't think you need to flush the DI filter.
I think the pressurized tank is fine, except that it might limit the flow rate of water you're able to draw - it might take 30 mins to fill a 20 gallon reservoir through the 1/4" line that's probably coming from the pressurized tank. If that's not an issue then you're fine. For me, I like being able to fill my res while I watch it - in 5 mins or less. I think I'll get that with even a small pump hooked to 1/2" tubing. Also - I don't know if your pressurized tank is like the tank on my kitchen RO unit, but the actual water storage capacity is less than the size of the tank due to the trapped air which provides the pressurization for the tank. I'd guess you'd lose a gallon or so.