Was the pamphlet sealed when released with the N64? 
Although i cannot say 100% i believe it came sealed. Do you have the Pokedex which holds the CDs with yours? I have 2 separate copies. One completely sealed and one with only the very outside wrapper open. However i cannot say 100% if this is the original outside wrapper.
@collect, I can confirm that the Pokedex with the CDs is sealed because I once had a lot of them (only kept one for me), but I just got the pamphlet and I dont’ know if the plastic seal is the orignal or if it was added by the japanese seller to protect it