Pulling from valley pan .. no baffle .. i would put on valve cover

Could you plumb it into the front of the valve cover with an upward facing baffle on the inside ?
I don't think that even the surge from braking would flood this , unless you are trapping a large volume of oil in the heads.

I agree.
All strokers have greater crankcase pressure cycling than stock: larger displacement in the same case volume. No, the pistons going the other way don't eliminate this, and there is also bay-to-bay pumping between adjacent cylinder pairs.

The valley is exposed to crankshaft throw-off. If it were the only source, it can be improved by adding a very tall vertical cylinder and pull from the top. The droplets will fall back and only mist will evacuate, but (duh) there's a space problem. Hint: the cylinder can have bends in it - the height is the important part. A vertical stub added to the valley going immediately to a 90° fitting, the a horizontal leg, 90° again should be able to bypass your manifold.

The valve covers are at least isolated from the crank, but still need to be masked/baffled inside (and in the separator) from flying droplets.

Is your dipstick tube sealed?

For both: a large diameter source (1"+) slows down vapor speed and encourages droplet fall-back.