Hello Craftseeker and welcome to the carnival!
I'll answer the easy question first: if an ally has "left town" (returned to the box), he is not available anymore, by any means! There's only one investigator that has an exception to this rule, the politician, but he's from an expansion. So, if Duke leaves town looking for greener pastures, you cannot gain him as an ally anymore. You can only gain one of the 11 allies that you randomly chose during setup and that hasn't been returned to the box yet.
Now, there's a lot of house rules on this, but this is how it should be played "by-the-book". Unimportant side-note: I play like this.
Further clarification: discarded allies return to the 11-ally deck, they are not returned to the box. So you can gain them again after they are discarded, just like discarded items returning to the bottom of their decks.
The other question is answered in the FAQ, page 8: Ignore all monsters and clue tokens at the new location. Monsters on the board are only dealt with during the Movement Phase. The investigator has a normal Arkham Encounters Phase at the new location, following either the "Gate" or "No Gate" instructions on pages 8-9 of the rulebook.
So, the investigator wouldn't have an encounter, he would enter the gate, but he wouldn't be delayed!