Drill for valves from above, or thru cylinder?

[Rod Cole]

I got the bore cleaned up as per the other thread. I did the bottom flange in the same set-up to get true squareness and am now looking at the valves. I cleaned up the top for the layout dye & may re-due the scribing (seems less than perfect in photo). The question is for someone who's already been there. Would you drill & ream for the valve from the top or thru the cylinder? If you look real close, it seems to me that something in the casting is off, the intake & exhaust flanges don't line up just right in my opinion which makes me worry that the boss for the valve & the port in the cylinder top might not be in alignment. What do you think??