Sryder I would suggest at least a 3000 gph, perhaps a little more if it were BB. Yes the stems would go all the way down on a BB.
The concept of filtrations in Reef tanks pretty much fall into two catagories with some crossing over. The filtration is always to deal with waste and detritus. On one handd you have those that rely more on biological means through the use of LS and LR for the processing of the above, call it kind of a aquarium composting. The other form are for those that rely more on mechanical filtration, they design thier system to keep the waste/detritus in the water column so that it can be removed through the overflow and them skimmed (and/o simular) out. So to answer your question if you have a BB system your first thougths must be to remove the waste/detritus. To do this you dont need a ton of flow just enough properly directed flow to do the job. If you feel that the flow is bothering your LPS and softies then just break it up more so it is not direct but still does the job you need it to do. So an example would be instead of having just two outputs on the end of the stem you could attach locline Y's to each and break it down to 4 outputs and get more coverage with out haing flow directly hit the corals, also stuff like bouncing the flow of the sides of the tank helps to.
Mike