nope, the flywheel and pulse coil are differnt on the 98-99 srx engine, the pulse coil is relocated on the viper case as the flywheel is smaller therfore its in a differnt location. You could with some machine work do the swap, simply move the pulse coil mounts to accept the larger flywheel, this will involve welding new tabs and drilling and tapping them to accept the relocation, if you sit both of them side by side you will see what I mean. If you were not so far away, I have a perfect shape srx 98-99 bottom end sitting here, would have traded ya for the viper.
forgot to add, that the stators themselves will bolt onto each case, but the magnets on the flywheel are differnt and if you would run the viper flywheel with 98 stator the timing will be all screwed up from magents on outside of flywheel are all differnt for the 3d ign. system.