Hey Sam,
If you are doing a tipup, the frame and the stiffener kit (those thingies with the holes) comes down into the space behind the panel. If your instruments are too high, the canopy frame may come down on them, especially near the ends. I was very glad I allowed at least an inch.
Most of the new radios have their own cooling blowers or don't need them, so ventilation is not usually an issue.
Paul's right about the box below the VCC. You don't see it in the photo I posted, but I have a small hole drilled in the panel below the VCC to adjust it. I hid it under the tag holder for the compass deviation.
Roberta