Its been a while Tina, and I had to find that quote of Naj's and see what context it was made, ( these threads involving HPR's tend to be like our dogs and go off in all directions

) Having a solid sit/ stop aids confidence in the handling of the dog, especially in handling the unexpected, which with the novice handler and novice dog can be ( seem ) an all to often occurrence.
In your case I believe the dog has had more opportunities to self hunt, so in reining it back, it could be a long road if you went the route of letting the `bird teach the dog' that post flushing does not require the chase, or that the flush does not require the point first. So in this case, I would be doing much the same as your doing in building that important partnership and that you are in control of the hunt and not the dog. When I'm dealing with a flash point/ flusher scenario, you have to find a way/instruction to maintain the point longer, the `wait' command is very useful and unlike the sit/stop does not create a conflict with pointing and sitting. If you teach `wait' as a basic control command in and around the house and daily routines ( going through doorways, gates and feed time ) It is probably the easiest one to use both in command tone and calming tone depending on how the dog is reacting to the game in front of it. It also means that you are not wearing down or tuning out the more important sit/stop by its over use in so many circumstances, or with so many different tones and meanings

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The stop whistle or hand signal means just one thing, arse on floor, what I think Naj was referring too in that quote was the example I gave of how it can go wrong if your dog picks up a signal that you were not using correctly and open to a `thinking dogs' misinterpretation . My dog could have been `taught' to sit on point had I not realised what was happening. ( a little `conflict' can be used to a handlers advantage, but it must be used carefully, and only as an aid to getting further down the training route, NOT as a solution )
As Wullie said, the bird rising post flush should become the sit/stop command, which if your consistent with the sit/stop whistle post flush the dog will `pre-empt' soon enough if you reward that action. When I start to see the dog control itself from the chase, even if the dog does not completely sit, I would praise that action before applying the sit whistle, but it would still be applied to get a full sit till I was confident in the dogs understanding of the flush as a sit/stop command...with all levels of temptations
