Rod,
The hole for the treadle linkage that connects all the throttle linkage is round**. It is located in the upper left corner of the transmission cover plate**.
I found this diagram someone else did for a CJ-3A and I felt it had to be the same as the 3B. I also went out and did an "eye ball/tape measure" check and the numbers seem to be accurate. The pedals and steering column were in my way but everything seemed very close. That treadle (gas pedal) hole in the floor toe-board should overlap the upper left corner. See attached hole diagram.
** As noted above, the actual floor cutout is an extension of the transmission cutout. Mine appears to be somewhat oval; about 1" wide and roughly 2" long. However, the most important part is the hole is actually cut into the transmission cover plate. Do you have an original cover? You could attach it and then draw onto the toe board the outline and then enlarge it just a bit. As best as I can tell, my cover plate hole matches the 1 1/8" diameter from the posted diagram (it has a slot cut into it so you can slip in onto the linkage shaft under the treadle) and it also has a worn spot on the other side from when my linkage was loose and rubbing against the cover plate. I left the worn spot there since it wasn't that noticeable. The best image I have is from the pics I took of an unrestored '54 at one of the Reunions I attended. See attached Rhorke image.
On the hood hinge, are you asking how to attach the hinge itself on the underside of the hood? Does that mean you have a hood with no hinge? OR does your tub not have the pre-tapped holes in the cowl (just above the firewall seam) to attach the hood? That attachment should have a tapped reinforcement plate under the cowl that's welded to the tub.
Here's an image I took of Lawrence's '55 that's on the 3B Page:
You can see the gutter is under the hinge. and the upper half of the hinge is actually attached to the lip of the hat channel running along the back edge of the hood. Another view:
