This week's book giveaway is in the OO, Patterns, UML and Refactoring forum. We're giving away four copies of Refactoring for Software Design Smells: Managing Technical Debt and have Girish Suryanarayana, Ganesh Samarthyam & Tushar Sharma on-line! See this thread for details.
No, no, no. The "clip" template should simply copy the sequence number parameter to the output.
There aren't any XSLT constructs which can work on nodes in the output. And there isn't anything in your input document which can be examined to produce a numbering system (at least not from what I can see from your input document). So the simplest thing is to produce your own sequence numbers, which is anyway trivially simple to do in the sample of XSLT which you posted. You already did half of that by choosing the sequence numbers. The second half is to use them.