With TC1&2, I found you could delete the two route JA files, leaving the core and yardmaster, and have a fully working program. All you have are the ground textures, built in industries minus the track for them and portals, which need to be edited for different rolling stock. I also found that for some reason, opening a built in item for edit created a duplicate, even after committing. What I did was copy all the JA files from TRS2006 into TC, opened for edit, recommitted then copied the local files to an external hard drive. You could do that with the editing folder before committing as well. Once I had all that, I deleted the JA files from the game, leaving the core and yardmaster. Import the content from the external and delete what you don't want. Hope any of that made sense. Nice clean install minus all the stuff I don't use.
I also found TS2009 works great deleting the four built in JA files. The only thing I lost was the ability to alter water color. I tried the open for edit, copy somewhere else and commit thing but the errors where too much to correct on import so didn't go any further with it.
Hope any of this makes sense.