Do you need to notch for valve clearance, or just for flow? I've notched 390 bores to fit big valves in the past, but never to improve flow characteristics. That actually sounds like a great flow study subject, because I'll bet you would pick up some substantial flow if you did that.
The biggest thing to consider when notching the bores is where the top ring on the piston will end up at top dead center. You don't want to notch into this area, of course, and I'd probably recommend a .100" safety margin between the top of the top ring and the bottom of the notch. Also, you don't want to notch the bores so far that the head gasket hangs over the notch. Get the head gasket you want to use installed, and mark the top of the bore so that you don't undercut where the head gasket will be located.
Offhand I can't think of any other major issues. The block deck is thick up at the top of the bores, of course, so you should be able to notch the cylinders as much as you want within the previously stated constraints.