Had a machinist knock 3 mm off the top off the Tone block and now has good clearance with springs fitted for the cover to sit. couple of really minor things that I didn't take into consideration was that the trem-bar hole is at an angle and when the top was machined moved the center of the hole forward and only just allows the trem-bar in cleanly.
Also when planning where control holes went, didn't even think about how the trem-bar would interact with anything else on the guitar. When fully screwed in the trem-bar cant go past the tone knob. (Luckily for now it will only be joining its dusty fellow trem-bars in a drawer.)
Suppose your always learning as you progress.