no harder than swapping 94XJ motors. if you have any doubts, re-use your 94 sensors to make sure everything plugs in the same.
as for the intake, the 99 would be an upgrade. to some searching on here for it and you'll see what's needed.
i would keep the 94 exhaust manifold.
or if you want it real simple, re-use the 94 sensor, exhaust manifold and intake.
oh you'll also have to re-use the 94 distributor, because the 99 is going to be distributorless ignition.