The bolts are 5/16"-18 and the flange is half inch thick. I'm not too concerned about it sealing up. Should I? What do you feel the failing point would be?
The sleeves and thru holes isn't going to be too bad, just find the location and sink an endmill down on the mill.
As far as the ports not lining up or being the same size, I plan on cutting them undersized then working them to match the head a bit. Then I'll measure them and incorporate them into the model and program.
Reinventing the wheel is how innovations and advancements happen! I could copy someone else's design and call it a day but its still someone else's design. I need to be able to put my logo on it.