Ah, I think I see what happened, you went with the inlet diameter, not the maximum envelope diameter of 46.5 inches as opposed to the maximum envelope diameter of 38.4 inches for the J79. Another complication would be that the J79, except for the variant used on the F-16/79 has engine mounted accessories whereas the F100, and most military engines since then, has a single drive shaft to an Airframe Mounted Accessory Drive gearbox. Of course, the F100 has a rather higher mass flow which would require larger intakes. Yes, the F100 first flew on the prototype F-15 but that was far from a production-ready, de-bugged, engine and the testing on the F-15 revealed that the spec. requirements that the F100 with respect to imposed loads were vastly understated and it took a fair while to sort that out. That the F401, a "pushed" version of the same engine was cancelled probably delayed development, too, as its test engines were seeing problems before the test F100 engines were.
For the record, the F110 maximum envelope diameter also lists as 46.5 inches which makes sense as it was designed to fit the same installation envelope as the P&W engine. It was the third engine in the family developed, the first two being the F101 and CFM-56, and the fourth in the family, drawing elements from all the others, is the F118 in the B-2A and U-2S.
The earliest you could probably see a quick replacement engine for the F-4 would be the late 1970's with the F/A-18's F404 (and derivatives) and an equivalent of the PW1120 likely wouldn't be available, at the earliest, until then, and that with a very dedicated program after the F100 was debugged.