I cannot supply an actual answer but I can let you know my experience of migrating from ActivePerl to Strawberry Perl.

No major issues at all!
Like you, I had planned and thought and worried...but in the end there were a few modules that needed updating which were easy to identify.

However, unlike you I am not running a web application on a Windows box. Instead, I migrated a number of standalone scripts and simple Tk applications. I seem to remember it was Tk that caused most of the few problems.