i realize this is an old thread, but I happen to be working on a 6.3 site and dealing with this issue. Was there ever a resolution for exporting a module for use in another site that uses custom taxonomy types?
is the only solution to manually recreate the manual on the new site after setting up the taxonomy? of course the taxonomy will be different, but as long as my custom code isn't referencing them by that ID I should be ok...
but is there a better way to do this for 6.3?
while I'm at it, what's the story for this in the latest 9.2?