You state that this is a fresh rebuild. The first thing that comes to mind is that the rings may not yet be fully seated resulting in slightly excessive blowby. This can be checked by a cylinder leak down test. If you remove a valve cover while a cylinder is pressurized and listen for any airy type sound to confirm possible blowby.
If you are into fancy oils or use a current spec automotive oil it is possible to retard ring bedding. Change to a quality four-stroke motorcycle specific mineral oil such as Castrol Grand Prix for a few thousand miles (or forever). (let the oil debates begin)
For the past few years I have come to rely on two gasket sealers, Permatex/Loctite Motoseal as a general sealant and Permatex/Loctite copper for head gaskets. I apply the thinnest possible smear with my finger over the entire gasket surface. The motoseal is very similar to Yamabond and other quality sealers but I find it more easily found here.
Assuming your problem is mainly at the base gasket there are a couple of areas overlooked by a number of rebuilders. The first is at the studs. Aluminum deforms rather easily and whether using studs or cap screws, they will raise the aluminum when tightened and modern practice is to countersink or counterbore 40 or 50 thou. the next time you pull your barrels remove a stud and feel for a slight rise from dead flat at the threaded hole. This can be removed with a small countersink in a drill (go real easy) and then by drawfiling to ensure flatness. Stuff rags to catch any bits and apply a bit of grease to your tools to capture most of the bits of Al.
The second leak source that I have found is at the joint of the two crankcase halves. I have found that ocassionally, for some reason or other, one case half will not be true to the other by about half a thou, again this can be solved with careful drawfiling after all the studs are out.
All this said and done, I have seen some real leakers fixed by positive crankcase ventilation. You can effectively use an automotive power brake booster check valve available for about 5 bucks at you local auto parts store.