I too had problems with the AP/Waggonz c90 pack where the scenarios would cause a SBHH everytime ... I asked for support from AP & one of the suggestions was to slim down the ol' Kuju folder ... Rather than fuss about wondering what to get rid of I followed advice from elsewhere on the net and copied my WHOLE Kuju folder elsewhere, to a 1TB external drive in my case & renamed it something like 'Kuju Archive' ... the simple thing to do then is choose the 'verify' files option in TS2013 from within the Steam menu, this will give you back a default kuju folder with just the basics plus anything required by the stock packs you've purchased from Steam ... That should get the c90 up and running, about 4GB it became down from 10GB in my case ...
Of course your 3rd party sceanrios & even other AP extra stock packs will now cry out for items from the old Kuju folder when you try to run them, RSTools will tell you what's missing from problem scenario, it's just a case then of copying what you need, when you need it from your old Kuju folder (safely moved elsewhere) and copying the stock you need back into the new, slimmer Kuju folder !
I'll add that to be on the safeside myself I deleted my whole WCML folder before running the 'verify' files option just to be extra sure things went ok, so if you follow the above & still have issues you could try that also, I then re-installed the c90 pack, all my previous AP purchases and extra stock, plus anything purchased from Just Trains & 3rd parties just to make sure the basic stock from those packs was back in the Kuju folder
I've removed all the repaints I don't use by now and have a nice archive of everything I've previously installed should I need it later on, I'd imagine that installing any of the 'free' packs from UKTS will start filling up the Kuju folder once again, maybe RSC can work on the core software to allow it to deal with these big directories ? Or do something to smooth the software out so it loads what it needs etc ... hope this helps anyway !