The whole point about using a standard CPAN module like Text::CSV(_XS) is that someone else has already figured out how to do all the things you listed -- and that code has already been debugged and tested -- so all you need to worry about is learning to use the module correctly.

Plus, there's probably a few things you hadn't thought of yet, and there are some choices you might like to have available as options. The module will support those things too.

... I'm ... concerned about why these regexs are so expensive.
... 98% of run time is tied to these regexs.

We see data being read and munged in the code shown in the OP. The inference I draw from the OP is that the only code not shown is to open the file, write the munged data and close the file. As such, there's almost nothing happening other than data munging done by regexes and, as jwkrahn points out, a possibly expensive string prepend. I don't understand why one would expect the great majority of time to be spent other than in regex execution given the length of the strings involved.

... my substitutions ... are slow.

But what does 'slow' mean? A day? An hour? A minute? My guess is that the regexes shown in the OP would take on the order of a minute or so per file. Is this MajingaZ's experience? How fast do they need to be?

I was recently tasked with making CSV files from a list of tab delimited files.

This is a trivial text processing task for which Perl is ideally suited.

I slurped the file as they are about 10 Megs and I do my substitutions, but they are slow.

Don't do that. There's no good reason to slurp whole files into memory in this situation. It just makes the task more complicated and is undoubtedly causing the slowness you're observing.

The following Perl script should perform the conversion correctly and be plenty fast enough.

#!perl

use strict;
use warnings;

use English qw( -no_strict_vars );

local $INPLACE_EDIT = '.bak';

while (<ARGV>) {
    s/"/""/g;
    s/\t/","/g;
    s/^/"/;
    s/$/"/;
}
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It looks like $file = '"'.$file; would be really slow because you are copying the entire file.

Anyway, it looks like you only need one regular expression (and transliteration):

my $file = <$INPUT>;
$file =~ s/(?:(?<=^)|(?<=\t))([^\t\n]*)(?=[\t\n])/"$1"/mg;
$file =~ tr/\t/,/;
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#!/usr/bin/perl

use strict;
use warnings;

my $filename = 'file.tabs';

local @ARGV = ($filename);
local $^I = '.bac';
while (<>){
    chomp;
    $_ = join(',', map {qq{"$_"}} split "\t") . "\n";
    print;
}
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