For something on the order of 100 MB that's a lot of work, and as simple as the task is I'd just write it in C. But if you want to keep it in Perl, there's one bug and a few optimizations that comes to mind:

• You have to chomp the lines first or CR/LF characters will always fall in the "bad character" range.
• foreach(split //) is a lot faster than regexing yourself through single characters
• If you expect bad characters to be relatively rare, checking your line first with something like/[\x1-\x20\x7f-\xff]/to see whether it even makes sense to go through the line character by character would speed up things enormously.

However, I think your right the whole task needs to get clearer. You say it's unknown what the encoding is supposed to be, but are you sure you're dealing with an 8-bit character set? As you wrote it, it would probably work for ASCII but not much else---anything from the Latin-x family (and many other charsets) may contain characters >126. The "ISO 8859 Alphabet Soup" might help visualizing what you want to check for: czyborra.com/charsets/iso8859.html

Edit: fixed character range typo as per jimw54321's comment

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