ayeronnie,
I guess I was lucky. I moved from MT 3.2 and found that after migrating to WP, the URLs for individual posts were of the same length (but for the .html extension, of course).
If it were me, I’d try something like this:
1. Export from MT.
2. Import into WP.
3. Export from WP.
4. Delete all the posts from WP. There’s a plugin that will do this in one step.
5. Go through the WP export file and change all your internal permalinks to the WP format. With regular expressions, this may not be as time consuming as it sounds.
6. Reimport from the edited WP export file into WP.
If this works, internal permalinks will be good. I don’t know how to get external permalinks pointed in the right direction. Maybe you could have a Rewrite Rule that redirects any URL that ends with “.html” to a page that explains the problem and asks the visitor to use the search field?
Good luck!
