Like a lot of these things, it depends on your point of view.

Most would say that the second Clone Saga began in Web of Spider-Man #117, with Peter Parker coming face to face with his clone, Ben Reilly. That issue even features the blurb, "Beginning the saga that will rock the Spiderverse" on its cover, so clearly Marvel considered this to be the start of the 2nd Clone Saga. This is also the point where the semi-recent Epic Collection TPB Spider-Man: the Complete Clone Saga, Volume 1 begins.

However, the lead-in to the Clone Saga began some months before that. Ben Reilly had been making mysterious appearances in various issues of Amazing Spider-Man, Spectacular Spider-Man and Spider-Man in the months prior to the publication of Web of Spider-Man #117...you know, visiting Aunt May in hospital, visiting Gwen Stacy's grave etc. It was also actually in Spectacular Spider-Man #216 (which leads straight into Web of Spider-Man #117) that Peter Parker actually first comes face to face with his clone. The meeting of Peter and Ben is that issue's big cliff-hanger.

So, personally, I tend to consider the '90s Clone Saga to have starting bubbling up in Web of Spider-Man #113 and #114, which is a two-part story in which Aunt May receives a mysterious phone call from someone who tells her that all is not well with the Parker family (this is the very first, shadowy cameo appearance of Ben Reilly). This plot point then builds until Peter and Ben eventually come face to face in Spectacular Spider-Man #216, with the story continuing in Web of Spider-Man #117.

So, the short answer to your question is, the lead-in to the Clone Saga began in Web of Spider-Man #114 (July 1994), but it didn't start in earnest until the final pages of Spectacular Spider-Man #216 (September 1994), and is usually cited as having begun in Web of Spider-Man #117 (October 1994), which follows on from SSM #216.