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1) Disable Clean URL while installing - Check in the Database for 'clean_url' - it should be 's:1:"0";' 
2) Default Timezone should be ZERO I.e UTC +0000 and keep default country NONE
3) Leave "Check for updates automatically ", "Email notifications"  as it is.
4) Delete cache_menu item INSERT (not table) 
5) Delete all watchdog INSERTS And also change its AUTO INCREMENT =1 ; 
6) We copy the original update.php from zip and add the following lines for upgrading from Drupal 6: 

// Softaculous Change :
$update_free_access = true;
7) Change the version of Drupal 6 in the upgrade.php and <min_require> tag in info.xml if there is an upgrade in Drupal 6 branch.
8) Dont change 'datestamp' to timestamp in DB. It is the launch date
9) We do not copy .htaccess from /sites/default/files/.htaccess because Drupal creates it. (Added scopy since 7.53 as it was not created automatically)
10) In next update change the datestamp to a variable  [[datestamp]] and update the datestamp everytime in install.php
11) Try to detect if Clean URL will work and update accordingly in database
12) Delete INSERTS only from the below mentioned tables from next version (i.e post 7.50) onwards :

cache
cache_bootstrap
cache_update

These INSERTS should get generated on visits of the installation. Confirmed by Drupal team via email.
13) PHP REQUIREMENT LINK: https://www.drupal.org/docs/7/system-requirements/php-requirements#php_required