Editing Stock Issues

I've definitely warmed up to TS lately after writing it off in favor of MSTS/OR for the past few years but one aspect that still grinds me gears is how unnecessarily difficult DTG/Kuju/RSC/whomever came up with this system has made creating and editing scenarios. The ridiculous markers, all the flyouts, the difficulty of swapping stock etc. etc. really makes it a pain. Since there's no program like Conbuilder to bypass DTGs system I use RW Tools which is a fair replacement if not a bit overpowered (nothing wrong with that) for the task. I switched out some cars in a player consist and got a few error 53s but nothing that crashed the application. It also showed the stock was swapped so I figured everything was kosher. When I was finished I saved the scenario and fired up TS. Loaded the scenario and I got missing stock errors. Excuse me? I decided to edit the scenario within TS and of course the marker was hanging in the sky upside down in a yard, player train nowhere in sight. Rubbish. So I go back into RW_Tools and get some missing file errors for that activity. The supposedly missing stock has file paths that are definitely not on my computer such Railworks/assets/producernamehere/railvehicles/freight/boxcar/m/on/railworks/assets/producername/railvehicles/freight/boxcar/stock.bin just to provide an example. Figuring this had to be a glitch I loaded up TS again and tried the scenario. Same thing. Went back into RW_Tools and now the consist in question is GONE and I can't even edit it making the activity useless. What's going on here? This is pretty much why I've stuck to Euro stuff for the moment as since I don't live there it's all new to me. I can't play American scenarios unless I have American variety but TS has made everything so difficult I really just want to throw my hands up and go back to MSTS/OR. 
