In FS2002 to get the gear to go down/up on helicopters that I've downloaded I have to pause the game. Is there any way to fix this?

Not really. There is a workaround, though. The new Gmax Dauphin that's out has a gauge that automatically pauses and unpauses the sim when you press "G". I forget the name of the gauge, but I've successfully added it to other helos as well.