In my tests prior to release the only way I could solve the sinking aircraft was to do this. Not the Ideal solution I know but otherwise AFCAD seems to be unable to control the modified height.

Bird good news - sorry I thought you knew.
There's a prog called JaBBgl that now lets you change the height of any airport in a jiffy. I've used it for my old Leeds, Cambridge and Humberside sceneries and it works a total treat - one of the best little utils I've come across in ages.
Doug, you shouldn't need 2 AFCADs at all but I think this was Arno's short-term solution to the problem before JaBBgl. Obviously it's not needed now. In any case, apart from the AFCADs, in FS9 you put ALL the scenery files for an add-on scenery into its scenery folder. I've done this with my 04 Kai Tak but not the 02 version. And this included navaids (which was how I got the Kai Tak navaids working I think before anyone else had worked out how and was just waiting for Lee to do AFCAD ;) )
Also, I've not issued them, but I found after hours of experimenting ::) that the 02 type dynamic files (the ferries and fuel truck) which had to go in special folders in 02 also work when you bung em into the addon scenery scenery folder.
Good stuff eh? Makes it soooo much easier.