My output seems to be coming out in reverse order of how it is programmed.

I have no idea what you mean by that. Show the output you expect for a given input.

when run it says scalar value @binary1 better written as $binary1, what does that mean?

Use perldoc diagnostics to get a more verbose explanation:

use diagnostics;
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Another tip: Don't use quotes around your numbers when performing numeric comparisons. Change:

elsif ( $decimal < "256" ) {
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to:

elsif ( $decimal < 256 ) {
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See also:

perldoc -q convert
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