The original linkage that came with the car has a bottom clutch rod with a bolt looking piece on the end. The books show the rod having a pointer end that fits into the clutch fork. Which is right,

The original linkage rod did have a pointy end. It was made from from a piece of hex-stock, drilled & tapped.

Obviously, it would follow that the clutch 'fork' (Ford called it a lever) had a matching depression....not a hole. But even Ford replacement parts deviate from the originals. Frankly, all you need is something that pushes on the 'fork' without flexing much or falling off as you drive.

if its the clutch fork with a hole in it, are the 429's, 428's, and 390's the same?

No - Ford made dozens of different 'forks', which vary by engine and model year. Here again, just contrive the set of 'fork' and linkage-rod so they match. Lots of rods will work - you just need one that's long enough to fit and while still providing some adjustability.

Hope this helps. If you need part numbers for the original stuff, let me know.

Mr F