i plan on putting a skunk2 intake manifold on my '99 gsr, but i am not sure if the stock air intake will work. anybody know?

 

yes.

 

try to get a Si-R intake arm it goes quite nicely with the stock airbox, and not a bottlneck like the sohc arm. this is whut yours would look like since its a gsr with skunk manifold. you can use the sohc box also. HTH