You may have to update,I tried interlinking a 997 with 5.32 to a 998 with 5.41,it did not work till i upgraded the 997 to 5.45. There could have been other issues,but the upgrade fixed it.
Fyi on eithernet. you can select which sonar you want on which unit,it is a simple hookup. also you can select which gps source to use on each unit. so then you would not have to calculate waypoint offset. but you would need a puck on the bow for the bow unit.