Tie - Rod End

I have taken off my tie rod end and did everything I think right, counted the turns and put new one on with the same amount of turns.

I used a small jack to bring everything up and now the tie rod end goes in nicely but doesn't go through all the way by itself.

Should I use a hammer and hammer it through?

Or

Should I use the wrench and tighten the nut until the gap is closed?

I tried to push tie rod end through on it's own and it stops at the same spot so I know it's not going through because of a misline.

Help as soon as possible I'm doing it right at the moment and I need to move the van out of the way for the move tomorrow. It's getting dark outside now as well.

I
I tried to push tie rod end through on it's own and it stops at the same spot so I know it's not going through because of a misline.
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You mean you have tested the old tie rod end too and it stops at same place as the new one? If that is the case, then --probably a scratch made during dissassembly - I see no reason why you should not tighten the new one using the bolt. Do not hammer it in.
I also suspect you have been able to compare tapers of both old and new and that they are indeed the same....

I have changed tie rod ends on a "regular" basis on that car....and can't remember of such occurence but may be one or 2 times it did not seat completely on itself by a small margin and I just bolted it in.....

..counting the turns is OK but if you notice the new position of the steering is different from what it was before, then come back here for a low cost toe-in procedure.....