Yea it seems like it was supposed to be available at the start of the game but as soon as Cid shows up at the place in your spoiler all of a sudden I could upgrade all of my weapons, one of a time very slowly of course.
There was no update or any sign showing I could, I was just luck enough to check at that time. I thought it was a glitch but I guess it wasn't.
This was going to be my follow-up question, so thanks for answering that.
I had noticed that I picked up several upgrade items and was planning to turn them in. Much to my surprise, Cid would only take one (at least initially; haven't gone back to him yet). I wasn't sure if you could only upgrade one at a time, or if I hadn't picked up as many upgrade items as I thought.