Just to give you folks an update, it took me long but I finally got rid of the brutal harsh 2-3 upsift (thump) at Wide Open Throttle on my 46RE.
I had to go down to a 0.115" orifice plug put into the aluminum transmission case at the direct clutch port.
I had tried larger sizes orifices before with little or no difference, such as, 0.140" then 0.125"and finally 0.115" when I got the harsh hit reduced to what I would call a real firm shift (clutch apply) but I am only talking about 2-3 upshifts at WOT, other than that the shifts were fine without the orifice plug.
It really made the difference, I can't believe that later year 2000 46RE's still could benefit of a direct clutch restricting orifice plug, because other than that, the transmission was fine.
Anyway, I am happy I do not get a flare in any situation. Still would like to go one size smaller (0.105") but really do not want to mess with the Valve Body, seals and screws any more.
Hope that helps someone with real harsh wot 2-3 upshift, best hint is start with a 0.110" orifice, you will probably have to replace it but then you know it is small (if you get a flare) or still large if you still get the thump harsh shift.