With MSTS?
There are a ton of fixes on train-sim.com for broken couplers and physics updates. You can also get another updated version of the NEC there.
If you are bound and determined to mess with the editor to "fix" the route, there are help files there too.
One great update is the unofficial 1.6 patch. It really improves the way MSTS handles lighting and graphics, updates the displays, and fixes a few other MSTS quirks. I have had the game for a few years and this really changed a lot.