After installing JFKV2 i noticed the gate numbers are all off. For example gate numbers starts at 101 - 846 in the FSX
That's exactly how they are supposed to be in FSX. FSX doesn't allow naming conventions to allow something like "Terminal 4, Gate 30B", so such gate would appear as "Gate B 430" in FSX. This standard has been used by many other developers too.
Of course, this is clearly explained in the JFK manual at Page 9, which also explain how you can also use the GSX menu instead, which is far more flexible and allows for parking to be named as in reality, which FSX doesn't allow.