Have you started out by looking at satellite photos? You can get a pretty good feel for what a river is like that way, though you have to have enough familiarity with rivers in general to figure out whether you are looking at low water or high water.
I just “flew over” much of your planned route using the photos on Google Maps and saw numerous short, Class I riffles, usually with very long pools between them. The current looked moderately slow in the pool areas.
I didn’t “fly” the whole thing, but most of it, and I saw only three dams, all on the lower section, and the ruins of a dam at Harper’s Ferry. Interestingly, the river seemed to dry up at that point, as if most of the flow had been diverted somewhere, though perhaps the all the tiny channels in the rock were enough to carry the flow. Still, the water below the confluence with the Shenandoah really looked too low, as if the water in the Potomac might have been diverted.
I might have missed a dam or two when occasionally skipping to map view while flying over the upper parts of the trip, though I saw no evidence of dams there by that method. Of the three I saw on the lower part of this stretch, the first two had an obvious easy portage on river left, and it looked like the best portage for the third dam was on River left as well, but with the take-out obstructed from view by trees. It looked like river right would be a tougher portage in all cases due to tall retaining walls both upstream and downstream of the dam on that side, but maybe there’s a guide book or something that will tell you what to do at the dams.
The usual problem with “low flow” when talking about whitewater is simply getting a boat through those spots. Why do you say shallows would be no big deal on a SUP? Is it because you can remove the skeg? If you can remove the skeg, do you have no concern with dragging your SUP over rocks? I assume you’ll be dragging and not carrying if you are packing camping gear, and I’d think that dragging a SUP would be more awkward than a canoe or kayak. If you can’t remove the skeg, I’d expect you to have occasional problems in many of the riffles unless the water is well above the low-flow conditions I saw in the photos, but you may be aware of that since you asked about recommended flows. Again, checking with guide books should help (in the area I live, any river that size would be well described in at least one guide book). Some of the riffles in the stretch approaching Harper’s Ferry get pretty expansive, but they look deep enough (until you reach the point where the river seems to go dry). On that note, the geology that’s visible in the river from the air in that lower stretch is pretty fascinating - you can see an endless series of lines where layers of rock intersect the ground surface and are visible in the shallow water, and you can see how the layers must be highly folded, or at least tilted.