Sometimes in FS98 while putting the gear up or down and the flaps up and down they take a very long time to come out. The simulator rate is on normal but they move as if on Very Slow. Is there a a way to fix this without changing the simulator rate?

Yes, you can edit the following sections of the airfile:Gear - sec. 1004 cycle time nose/tail, left, rightFlaps - sec. 1001 flaps cycle timeckfly

If the aircraft has been used in fs2002, I believe you can adjust the flap extension time in the aircraft.cfg file under the flaps section.