Moving to Patch 6 is tested and more than recommended approach due to inherent security holes in Patch 4. I believe this was suggested long back, and various organizations have already performed it. Go ahead and apply this patch w/o any further delay.
The steps as outlined in the doc are pretty straight forward, stpes might vary based on environment setup, however as far as patch is concerned, everyone has to follow the basic as suggested.
I've done this migration quite a few times, including for some large customers.
First off, I'm a big believer in not using the migration scripts at all. This is for several reasons:
1) Look at the release notes and migration guide. Find the list of stuff the migration tools don't migrate. If you have anything configured in that list, you're doing a manual migration anyway. You may as well go soup to nuts and do it right.
2) Can you configure your current Directory installation from scratch, parameter by parameter? If not, you shouldn't be doing anything to it besides studying it. If you can, then you should be able to configure the new version similarly.
3) New version means new features. How can you assess which new features will benefit you if all you do is blindly migrate your old configurations?