How to debug maps which use custom extension XML ?

Hello , 

We have lot of  complex mapping which uses custom extension xml .  

Usually when I want to debug map I just validate it and get the xslt and then  debug xslt using  Debug xslt feature of XML.

However if i try using similar way for maps using external assemblies I get error “Cannot find the script or external object that implements prefix ‘http://schemas.microsoft.com/BizTalk/2003/ScriptNS0’.” 

The maps are really complex and I need to debug them to find issues.

Can someone please help me with this ? How do you deal with such mapping ?

Thanks in advance 

madhu