Thanks all. Terry, your help is very much appreciated.
First off, I'm aware of the cooling holes but decided not to bother because, as you said, they won't be seen because of the close proximity of the pilot's seat back and the wing spar.
As to the mystery box, I suppose it's possible that, at some point, the control panel/unit moved from it's specified position behind bulkhead 4 to the wing shelf but I had assumed up to now that it remained there. See the figure from the manual below.
I had always associated the control panel with the control unit. Note also the location and shape of the switch panel just above the indicator unit. This panel, part of the Gee system, shows up in the schematic drawing in the manual above (you can just see part of it at bottom left above). It is also described in the manual, in words, as being mounted above the indicator unit.
The information I received from Dave Wadman suggests what you said earlier, that the "mystery box" is the IFF T/R. He included the same picture as you did in post #67 which shows the T/R and its associated switch box. To my eye, the switch box in the picture in post 67 is the same as the one mounted above the indicator unit in the last picture of your post immediately above. So that would mean that the Gee Switch box was moved and may have changed in style at some point (if the drawing you included in post 67 purports to represent the various parts realistically, then "Switchbox Type B" looks nothing like the one I posted above).
The reason I'm not yet convinced about the mystery box being the IFF T/R stems from 2 concerns:
1) the size of this box is quoted as 12" high x 12" long x 9" deep with the face showing the letter "D" in your picture pointing toward starboard. The associated switch box is stated as being on the
starboard wall next to the Observer, not, as suggested in your picture, mounted on the port canopy rail.
2) I have a copy of the DVD "Mosquito Explored" which shows the same IFF T/R unit mounted out of sight in the mid-fuselage near the TR 1143 unit in Mosquito NF II s/n HJ711 (that's the same specimen represented by your pic of the Gee system immediately above).
The Mosquito explored DVD also shows this:
It goes on to identify that the Gee junction box is at left (makes sense - shown as such in the manual diagram above) and the Gee receiver being in the center (WRONG!!!!). The box in the center is clearly NOT the Gee receiver; that's the unit at right. What's more, this is the same aircraft as in your picture above, an NF II, but I suspect it was taken at a time when the aircraft was part way through restoration. Note that the Gee receiver is mounted on wooden blocks and there is no interconnecting wiring anywhere. Now, if you look closely at the "mystery box" and compare it to the schematic diagram you posted and the unit under your right yellow arrow, the connector configuration and grab handles do strongly suggest that the box is, in fact, the Gee Control Panel (Unit).
So, it would seem that the NF II might have had the entire 3-box Gee set-up in the cockpit and the IFF T/R housed in the mid-fuselage with it's switch box up front above the Gee Indicator if we can believe the pictures and description in the Mosquito Explored DVD. However, the error in identification of the units doesn't help with credibility here.
I'm going to let all this marinate for a bit yet and make a decision soon.
Thanks again Terry.