In 1969, J tells young K that in 25 years he will pick him to be his partner, which is 1994 and 14 years after that, Boris escaped... So, is the present part of the movie actually in 2008?
The movie transcript makes it clear that MIB3 is set in the year 2008.
Young Agent K: Last chance, Who are you and what do you know?
Agent J: I am an agent of "Men in Black" but I'm from the future. We're partners 25 years from now you're gonna recruit me and 14 years after, the guy you didn't let me kill at Coney Island he escapes from prison, and jumps back in the past and unleashes a full scale invasion of Earth. We have about 19 hours to catch him and kill him so we really need to go right now!
Young Agent K: [after a pause] Alright.
Agent J: So that's the story you believe?
1969 + 25 + 14 = 2008
Since the film was originally 'greenlit' in 2008 (and sections of the script and screenplay may well have been cannibalised from earlier scripts going back as far as 2002) it's not surprising that the dates would be a bit inconsistent.
There's also a reference in the original screenplay to Kay having waited forty years for a chance to finally kill Yaz (later renamed Boris);
Kay : I've been waiting forty years for another shot at you, scum.
Kay takes aim and... CLICK! Empty.
No, it's firmly in 2012.
Closer inspection of the movie reveals that when Jay and Boris are discussing years and time periods, they are frequently speaking in general terms, not exact figures. Consider the math in question, that 1969 + 25 + 14 = 2008. While correct, the premise behind this is flawed. Remember that the original movie was released and set in 1997, not 1994 (1969 + 25). So when Jay said "25 years," he meant it in a rough, "round-number" sense because it's actually 28 years.
If you add 14 years to 1997, you arrive at 2011, which is reasonable given that we don't know what months Jay is referring to and how the rounding would work out.
Right before the scene where Agent Zed's funeral takes place, the giant screen shows Agent Zed: 19XX-2012.
Many of the cars seen in the present-day parts of the movie did not exist in 2008. In particular, the sixth-generation Ford Tauruses used as the new MiB patrol cars were released in August 2009.
1969 to 2008 is 39 years, yet several times in the movie people say "more than forty years."