First, a couple nitpicks:

• You have a comment saying "read stdin and any/all files passed as parameters..." Actually, it should say "or" instead of "and" -- the while(<>) reads either from file names given on the command line, or from STDIN, not both.
• If you think you need to do print or die $! at all, you should do it on every print statement. (But you probably don't need to do it at all. When a print to STDOUT fails, you either don't need to be told, or else you'll get other error messages anyway.)
• Doing print "" is a noisy way of doing nothing at all.

All that aside, I think the device you're looking for is the "look-around" assertions in a regex. Here's a slightly modified version of your code (because sometimes I can't help but change things), with the relevant bits added in the final "else" block:

#!/usr/bin/perl 

use strict;
use warnings;

my @G1x_replace = (
    "M104 S0 ; laser off\n",
    "M400 ; wait for moves to finish\nM104 S100 ; laser on\n",
    );

while (<DATA>) {
    if ( /G1([01])/ ) {
        print $G1x_replace[ $1 ];
    }
    elsif ( /G92|M190/ ) {
        next;
    }
    else {
        s/(?<=G1 Z)(?=\d)/-/g;  # look-behind and look-ahead to insert
+ "-"
        s/E[\d.]+ //g;          # no look-around needed, just delete s
+tuff
        print;
    }
}

__DATA__
G92 E0 ; want to remove all G92 lines (works now)
T1
G1 Z0.050 F7800.000
G10 ; retract
G92 E0
G1 Z0.150 F7800.000
G1 X14.725 Y-8.975 F7800.000
G1 Z0.050 F7800.000
G11 ; unretract
G92 E0
G1 X14.725 Y8.975 E0.01465 F120.000 
G10 ; retract
G92 E0
G1 Z0.150 F7800.000
G1 X-9.585 Y-0.615 F7800.000
G1 Z0.050 F7800.000
G11 ; unretract
G92 E0
[download]

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