I usually use this config for perltidy that mirrors (mostly) the recommendations from Perl Best Practices (and it uses 4 spaces).

## PBP perltidy RC file
-l=78   # Max line width is 78 cols
-i=4    # Indent level is 4 cols
-ci=4   # Continuation indent is 4 cols
-st     # Output to STDOUT
-se     # Errors to STDERR
-ce     # cucddled elsen (XXX my pref)
-vt=2   # Maximal vertical tightness
-cti=0  # No extra indentation for closing brackets
-pt=1   # Medium parenthesis tightness
-bt=1   # Medium brace tightness
-sbt=1  # Medium square bracket tightness
-bbt=1  # Medium block brace tightness
-nsfs   # No space before semicolons
-nolq   # Don't outdent long quoted strings
-wbb="% + - * / x != == >= <= =~ !~ < > | & >= < = **= += *= &= <<= &&
+= -= /= |= >>= ||= .= %= ^= x="
        # Break before all operators
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At first glance nothing about your sample file there looks particularly egregious (although your usage of prototypes is maybe a bit suspect; in most cases unless you're trying to affect how perl parses things in a weird way you don't want to use them (that being said the new signatures are a slightly different story)).

Edit: Also after another closer read looking at what the code's doing rather than formatting it looks like you may be reimplementing an existing wheel (see e.g. Data::Diver).