I'm not sure how FastCGI actually works, but I could imagine that IIS launches the Mojolicious FastCGI process only on the first page request.
To check this theory, the performance of 4-5 seconds should be same-ish as the performance of your script running as CGI under IIS. Maybe you can also see in the process monitor whether your Perl script gets launched immediately or only after the page is first requested.
If the startup is the issue, I would consider adding a warmup script that fetches one or more pages via Mojo::UserAgent or whatever to generate a status message and to prime the process and eventual database connections etc.
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