Ktm 990 Counter shaft replacment

I have installed the new countershaft on my 990, and bought new fork shifts. Everything is cleaned and I want to close the two casings, but find that the new gasket looks different from what I took of the casings. Its fits perfectly, but the old gasket was in two separate parts.
Do I just fit the gasket and cut the rest off, or is this the wrong gasket?
Another thing is that the gearshift rail on the countershaft (long one) is not as free moving (up and down on the spring) as the shorter one, although it's perfectly in line.