When making up track sections, there may be a gap as much as 1/16 to an 1/8 inch. The smallest track section available is the 8mm 5208 (.315"). In order to close the gap, I plan to cut a rail from a bad track section the length of the gap, place a rain joiner on one end and use that to bridge the gap between sections. The third rail should still be in contact at that wide a gap. I'm in the process of planning my layout and won't get to find out if my rail connection works until I start to lay down track. The layout has been laid out on autocad and there are many gaps that are too small for the 5208 track piece. I'm thinking it will work. What do you think of my plan?

I think that you are completely off track (...).
Under no circumstances should it be necessary to cut M-track.
You obviously don't get the basic geometry of the track, and should study the catalogues more, where all the necessary information is shown and explained.
At close quarters (as in lots of points and parallel tracks) the geometry has all the necessary pieces.
At greater distances, such small inaccuracies as 1/16 and 1/8 inch can be joined directly without any problems.

If you can export a graphic of your CAD-layout and show it here, I can pinpoint exactly where one or another thing must be changed and/or where the track can be joined in real life without any problem.