You can't legally use those characters except in material commissioned and published by Pocket, IDW, or TokyoPop, because they're the only people licensed to publish Star Trek fiction in print form. All fan fiction is technically copyright infringement. But it's generally tolerated so long as the author makes no attempt to sell it for profit.
So the idea of asking for permission to use someone's characters in fan fiction is self-contradictory. You can do whatever the hell you want in fan fiction, so long as you don't try to sell it.
Though as of now, my tales are just fan-fic, I fully
intend to get them published.
Still, common curtosy would seem to demand that I at least go to you for some input on how to treat characters you've created. I remember David R. George III noting how he and KRAD "gave" each other characters for their respective "Lost Era" books.
I find it interesting how the writers who created the characters apparently don't have any real say in these matters. Interesting --and a little disturbing, if you ask me....