New ccgi site - .htaccess help

[#1]

Hi there - almost fixed everything!
Can someone advise how/if it is possible to fix and merge these two .htaccess files?
File 1:  default Joomla 1.5.x .htaccess used along with sh404SEF which used to work before the upgrade 
This does not seem to work any more since the upgrade :
#
RewriteEngine On
RewriteBase /
########## Begin - Joomla! core SEF Section
#
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.html|\.htm|\.feed|\.pdf|\.raw|/[^.]*)$  [NC]
RewriteRule (.*) index.php
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]
#
########## End - Joomla! core SEF Section

File 2:  as advised by Gabe in a previous post using a phpwrapper to get around the ~userrname isuse. This is great and keeps  PhpGedView functioning correctly    but
on its own does not seem to provide all that Joomla requires in order to run sh404SEF :
# start
RewriteEngine on
RewriteBase /
#
RewriteCond %{REQUEST_FILENAME} -d
RewriteRule ^(.+[^/])$ $1/ [R,L]
RewriteCond %{REQUEST_URI} \.php$
RewriteCond %{REQUEST_FILENAME} -f
RewriteCond %{REQUEST_URI} !^/~username/phpwrapper\.php
RewriteRule .* phpwrapper.php
#  end

Any suggestions welcomed!
Stuart

[#2]

With the caveat that I know v little about Joomla and zippo about sh404SEF, I have a test install of 1.5.14 sitting in a subfolder with this .htaccess and the built-in SEF options seem to work for the example pages.

##
# @version $Id: htaccess.txt 10492 2008-07-02 06:38:28Z ircmaxell $
# @package Joomla
# @copyright Copyright (C) 2005 - 2008 Open Source Matters. All rights reserved.
# @license http://www.gnu.org/copyleft/gpl.html GNU/GPL
# Joomla! is Free Software
##

#####################################################
#  READ THIS COMPLETELY IF YOU CHOOSE TO USE THIS FILE
#
# The line just below this section: 'Options +FollowSymLinks' may cause problems
# with some server configurations.  It is required for use of mod_rewrite, but may already
# be set by your server administrator in a way that dissallows changing it in
# your .htaccess file.  If using it causes your server to error out, comment it out (add # to
# beginning of line), reload your site in your browser and test your sef url's.  If they work,
# it has been set by your server administrator and you do not need it set here.
#
#####################################################
##  Can be commented out if causes errors, see notes above.

#
#  mod_rewrite in use
RewriteEngine On
########## Begin - Rewrite rules to block out some common exploits
## If you experience problems on your site block out the operations listed below
## This attempts to block the most common type of exploit `attempts` to Joomla!
#
# Block out any script trying to set a mosConfig value through the URL
RewriteCond %{QUERY_STRING} mosConfig_[a-zA-Z_]{1,21}(=|\%3D) [OR]
# Block out any script trying to base64_encode crap to send via URL
RewriteCond %{QUERY_STRING} base64_encode.*\(.*\) [OR]
# Block out any script that includes a <script> tag in URL
RewriteCond %{QUERY_STRING} (\<|%3C).*script.*(\>|%3E) [NC,OR]
# Block out any script trying to set a PHP GLOBALS variable via URL
RewriteCond %{QUERY_STRING} GLOBALS(=|\[|\%[0-9A-Z]{0,2}) [OR]
# Block out any script trying to modify a _REQUEST variable via URL
RewriteCond %{QUERY_STRING} _REQUEST(=|\[|\%[0-9A-Z]{0,2})
# Send all blocked request to homepage with 403 Forbidden error!
RewriteRule ^(.*)$ index.php [F,L]
#
########## End - Rewrite rules to block out some common exploits
#  Uncomment following line if your webserver's URL
#  is not directly related to physical file paths.
#  Update Your Joomla! Directory (just / for root)
RewriteBase /folder
RewriteCond %{REQUEST_URI} \.php$
RewriteCond %{REQUEST_FILENAME} -f
RewriteCond %{REQUEST_URI} !^/~username/phpwrapper\.php
RewriteRule .* ../phpwrapper.php 

########## Begin - Joomla! core SEF Section
#
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
#  RewriteCond %{REQUEST_URI} !^/index.php
RewriteCond %{REQUEST_URI} (/|\.php|\.html|\.htm|\.feed|\.pdf|\.raw|/[^.]*)$  [NC]
RewriteRule (.*) index.php
RewriteRule .* - [E=HTTP_AUTHORIZATION:%{HTTP:Authorization},L]
#
########## End - Joomla! core SEF Section

My install is in a subfolder, so the rewriteBase is /folder and the phpwrapper file is accessed via ../phpwrapper.php, i.e. one folder up.
Gabe

[#3]

Thanks for your advice,  Gabe,
I'll give it a try but I am now trying to resolve some other issues so have backed all by .htaccess changes out for the time being 
Stuart