Most of the second and third lines are devoted to initializing $a (and $| as a side effect):
||=join'',map--$|x$_,(unpack'w',unpack'u','G^<R<Y]*YB='
.'KYU;*EVH[.FHF2W+#"\Z*5TI/ER<Z`S(G.DZZ9OX0Z')=~/./g
The two unpacks generate an array consisting of the number 14417713111218131332253147132969324349431334211136532212511512172112293224231453242.
The decimal digits of this number are then extracted via =~/./g and used to run-length decode a bit string 1000011110... via map--$|x$_. Since the number of decimal digits is odd, the last value of $| is 1.
After we remove the initialization code and the trailing #JAPH, comment we have:
{$_=pack'B8'x25,unpack'A8'x32,$a^=sub{pop^pop}->(map substr
(($a)x2,$_,256),7,249);s/[^\w,]/ /g;$ \=/^J/?$/:"\r";print,redo}
The expression substr(($a)x2,$_,256) produces a copy of the bitstring rotated left by $_ characters (assuming 0<=$_<256). The map sets $_ to 7 and 249 producing the bitstring rotated left by 7 characters and rotated right by 7 characters respectively. These bitstrings are passed to sub{pop^pop} which XORs them together. They are then further XORed with the original bitstring.
The unpack separates the bitstring into groups of 8 bits, and the pack converts the first 25 groups into characters. The substitution converts everything but letters and commas into spaces. The next statement sets the output line ending to a CR unless the first letter of $_ is a J in which case it sets it to the input line ending. The final redo starts over at the beginning of the block.
The rotate-and-XOR operation used in this program has period 128, so every 128 iterations the JAPH string is printed. The initial bitstring becomes the JAPH string after 67 iterations. I note with interest that the bytes after the end of the JAPH string are not all binary zeros.
