It will not be an easy task. You could use upgrade utility and generate new code, but don’t expect that code to be efficient.
Ideally for every adapter you use in 4.x, you should identify a methodolgy that you may use in webMethods 6.x.
The upgrade guide from webMethods is a good starting point.
One of the lessions we have learned is to make sure that functional specification and test cases for existing integration available, so that when the integrations are upgraded in 6.x (using any method, upgrade utility, or manual code rewrite), they can be tested to verify the functionality.