If you just want "the values", then keep them as strings. If that seems problematic, you have to show some code where you show how you acquire the data (say, from initializing a string), how you unpack it, and what you want to do with it in the end.
If you want "the values" as "number", then you have to unpack them from the string. As long as you are dealing with four-byte numbers, or your Perl and the C program have the same interpretation of the long type, there will be no loss of accuracy.
As for your questions about alignment etc., that is what Convert::Binary:C is set up to handle.
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