The hardest part of converting a recipe stated in volumes to baker's percents is indeed the flour. The water is usually less of a problem. Technically, a cup of water weighs 8.33 ounces. However, if I eyeball a "cup" of water, I usually get 8.1 to 8.2 ounces when I weigh it. In doing water conversions, I use the latter on the assumption that others eyeball a "cup" of water the same way I do.
To give you an idea of how I try to convert recipes stated in volumes to baker's percents, some time ago I decided to try to come up with a set of baker's percents for one of fellow member buzz's very good deep-dish dough recipes. If you read the first 14 replies at http://www.pizzamaking.com/forum/index.php/topic,1184.0.htm
, you will see the steps I took to try to divine buzz's technique for measuring out the ingredients for his dough. Subsequently, I devoted a good part of another thread to trying to reverse engineer buzz's recipe to come up with a set of baker's percents. I don't know if by doing this I captured the essence of buzz's recipe and dough, but I think it is safe to say that one would have to make several attempts to arrive at a finished product that would be very close to buzz's. If buzz had and used a scale, his formulation would most likely be better than any that I could produce since he would be using his own practices, which no one else would be likely to replicate with the same degree of accuracy unless they are in buzz's kitchen watching him at work.
On the matter of making mid-course corrections with a recipe, my practice is to note the extent of those mid-course corrections. I do this by noting how many teaspoons or tablespoons of flour and/or water I use in achieving the final dough results, and then go back when everything is done to adjust the formulation to reflect the changes in the baker's percents. Theoretically, changing the amount of flour should call for adjustments to the other ingredients also (other than the water), but usually such adjustments would be so minor as to be inconsequential to the final results. I suspect that most people don't readjust the baker's percents to reflect mid-course corrections, but by doing so I think you do move a bit closer to a more precise formulation. At that point, I would rely more on the baker's percent formulation than a volume formulation. And coupling the baker's percent formulation with a proper thickness factor sets the stage for doing the kinds of conversions that Slamdunkpro was asking about at the top of this thread.
An interesting side effect of the way I convert volume recipes to baker's percents is that when I convert the weights of flour back to volume measurements, my volume measurements are usually different from the ones I started with. This is because I specify the precise way I convert weights to volumes in the baker's percent formulation. And if a user measures out the volumes the same way as I specify, he or she is more likely to get close to my measurements and results. Most recipes stated in volumes are silent on how the volume measurements are actually achieved, and I think that that leads to a high error rate and erratic results, leading the recipe followers to scratch their heads over their results.