Change
s/^[ ]*//g;
s/[ ]*$//g;
to
s/^[ ]+//;
s/[ ]+$//;
to avoid useless substitutions. I also removed the /g since there's only one start of line and one end of line per line (unless /m is also used).

Are you sure you want [A,P]M (which matches "AM", ",M" and "PM") and not [AP]M?

The slash in \:000 is useless, but that won't affect anything (except readability).

The slashes before the ~ characters are useless, but won't affect anything (except readability).

If the file isn't too big to load into memory, you could try doing that.

local $_;

# Read entire file into $_.
{ local $/; $_ = <IN_FILE>; }

# Execute substitutions once each.
s/^[ ]+//mg;
s/[ ]+$//mg;
s/
   :000[AP]M
   |
   99991231
   |
   Jan\ 1\ 1900\ 12:00:00
//xg;
s/[ ]*~\t~[ ]*/~/g;

# Output entire file.
print;
[download]