For item 1 refer file frontaccounting.php in your webroot and comment out the lines below:
Line 18:
// include_once($path_to_root . '/applications/manufacturing.php');
and Line 80:
// $this->add_application(new manufacturing_app());
For item 2, edit the appropriate smarty template for the forms and edit the repXXX.php files for the PDFs/Excels
For item 3, make all your items 0 rated tax and see that your suppliers and customers are also in the default 0 rated tax. Then edit the necessary repXXX.php files for removing the ax lines.
There are lots of developers in the jobs section of the forum you may contact for your modifications. There are also a list of Support partners available in the Wiki.