This question depends on so many things:

1. What webserver are you using?
2. Did you write the SSI programs yourself? Do you have access to the sourcecode? Are they written in perl?
3. Do you have mod_perl?

If this were my project runing under Apache w/ mod_perl and the SSI scripts were programs that I had written; I would convert all the SSI's to perl modules and call them via mod_perl from the new .cgi programs.