In the past, I have found that XSLT can be an extremely powerful searching and filtering tool, as well as a good presentation/transformation tool. I cannot say for sure that it would work in your situtation (because I am not sure i understand your problem 100%), but it might be worth looking into. You may be able to kill two birds with one stone here too, using the XSLT to do the searching and HTML conversion. The trick with XSLT is to think declaratively, but given what I have seen you do with reg-ex's in the past, I doubt you will have any trouble with it. There is always X-Path & XQL (not sure what they are calling them now), which can do some really interesting stuff as well.

I always like to try and use other XML based technologies with XML, they tend to be a good fit, and they up the project buzzword quotient signifagantly too.