Your problem sounds like a "Flattening" issue.
CFS2 has an explanation in the installed documentation (see "Readme" doc in CFS2 main directory, pages 7 &

.
Due to how CFS2 handles terrains and elevations, the Flattening option basically takes your add-on scenery (i.e. FS98) and sets it to a certain elevation by specifying it as a four-point rectangle and the elevation. The flatten switch is inserted into the [Area xxx] description block of your Scenery.cfg file. It took me a couple of re-reads to understand the instructions.
You will probably have to play with a number of settings for the elevation and it may not perfect. You may find some of your terrains phasing in and out based on your point of flight. Use your "Shift-Z" option to get the Long/ Lat coordinates while in the add-on scenery and insert those into the Flatten switch.
Hope this solves your problem.
MH