Vim is creating a persistent perl interpreter that is lasting the lifetime of the Vim script

Actually, the perl interpreter is lasting for the entire life of the VIM instance, as evidenced by the fact that you can declare Perl functions in one .vim script and call them in a different .vim script.

This, of course, leads to the logical solution for the parsing-via-stand-alone-perl issue: move your functions into a module (or even just a required .pl script), and use the module in you .vim script. This would probably work out better in the long run than even in-lining Perl code in the .vim script and using the -x option, as you could then re-use the Perl code. Then, you'd need only create the VIM emulation module.

bbfu
Black flowers blossom
Fearless on my breath