I hope you have the correct upper arm. If I am correct, different arms have different diameter pins. You mention knuckle. So I assume your 4x4. If your 4x2, and you mean spindle instead, they make 2 different upper ball joint studs depending on your suspension (torsions or coil).
If it does fit, but just won't go in the hole, take the sledge to it? Maybe lube the hole up, makes it easier to slide your pin in.
Might have to undo a sway bar link to get the lower arm up further if thats your problem.
Other than that, I can't see how you can't get it in. After all, you got the old one out, and thats usually the hard part.