The if statement was not the answer to the issues unfortunately and the only reason it seemed to partially work before was due to other errors in code on my part.
After battling with the app all day today, I have just discovered the main source of the collisions in function __fud_login_common of forum_login.php.
This always calls db.inc in
if (!$GLOBALS['PATH_TO_FUD_FORUM_DB_INC']) {
require_once $GLOBALS['INCLUDE'] .'theme/default/db.inc';
} else {
require_once $GLOBALS['PATH_TO_FUD_FORUM_DB_INC'];
}
Temporarily got around this by moving that block under the preceding if (!isset($GLOBALS['FUD_OPT_1'])) { statement.
Looks like i'll have to create my versions of the two files to get around the collisions as I suppose understandably, they were never designed to be called in a situation where index.php is being loaded.
Done for the day. Bed beckons!