Here is what's happened so far. After all the abrasive and chemical paint removal was done, I washed the floor pan twice with AquaKlean with a thorough rinse of warm water after each application drained out through a hole in the floor to a bucket underneath. I then immediately dried the floor thoroughly with a heat gun and let it cool.
Then the RustBlast was applied and the whole area kept wet for 30 minutes painting it on and swirling it around with the supplied brush. No areas were allowed to dry out. Then the floor was rinsed with 2 gallons of warm water also draining out through the hole so the floor was left really clean. Then it was dried immediately with a heat gun.
Here's a small section of the floor showing some rust spots and how they changed after each stage of the treatment.
After the abrasive and chemical removal of the existing paint.

After the AquaKlean treatment and drying.

After the RustBlast treatment and drying

Notice how the brown rusty areas are increasing throughout the treatment and are particularly pronounced in the last photo after the RustBlast treatment.
As I said earlier, I'll gladly do more work at this stage if it will help improve the chances of long term success. I don't want to do all this work hoping it will be OK only to have the rust return in a few years time.
Should I re-treat the rusty spots with RustBlast for a longer period of time - say 1-2 hours?
What color should the rust spots be after RustBlast treatment? Do they go dark like when treated with a rust converter?
If I re-treat these rusty areas, will it be sufficient to just clean them afterwards with a wet rag rather than flood the whole floor and sub-frame again?
Many thanks for your help, Dave