I just talked with a fellow that put a Ford 289 into a BT7 about 25 years ago. He built his own headers. He does not recall cutting the foot boxes. He said the gas pedal was in the stock location.
As for the engine bay, a 100 and a 3000 have the same engine bay. The only real difference is that the radiator in the 100 is on the engine side of the front cross member. The rad in the 3000 is on the front side of the cross member. That's why the 3000 bonnet has a scoop ..... to clear the radiator.
A radiator in a 100 can be installed on the front side of the cross member, without bonnet modification, by slanting it down towards the front of the chassis legs. This opens up the engine bay to accept an in-line 6-cylinder motor. Or..... wait for it ........ move a V8 motor further forward for better footwell clearance in a 100/4?