Shatner's performance of Kirk did change over the course of the series. What we see in "Pilgrim Of Eternity" is much more like the third season Kirk than the first season.
I agree that elements from outside TOS feel odd in such a production, particularly those elements from contemporary Trek such as TNG. Mind you some of those things could have been tweaked. The Counselor could have been given a different title and her role could have been more like that of ELizabeth Dehner or Helen Noel and then she mightn't have seemed so out of place. The holodeck is so associated with TNG and contemporary Trek that it almost doesn't matter the concept was introduced much, much earlier in TAS (the same can be said for TNG's main theme which is really a lift of the TMP main theme).
I also agree with the stories. I think STC did a better job of it than anyone else, but there is something about a lot of the fan film stories that feels like contemporary Trek. It might be understandable since a lot of those involved in the productions could have been weaned on TNG and the rest rather than TOS.