Zend certified PHP/Magento developer

Magento 1.9.3, Google Analytics configuration – page views and transactions tracking problem

I would like to describe our problem with Google Analytics configuration. I have tried to find any solution here, in GA documentation and Google but nothing solve our problems.

Configured GA througth System > Configuration > API Google
We asked Google support why have huge difference between campaign statistics clicks and sessions/users on our page. Answer – tracking code not installed properly on every subpages.
Two options to select in type of analytics – Google Analytics and Universal Analytics. If I choose first option – page views from homepage not tracked, second option – page views from category pages not tracked. (page source – missing tracking code on these pages)

I can put tracking code directly in head section on every page and disable this module but… I will lost GA core plugin functionality like tracking events – adding to cart, transaction etc.

Please, give me some advice, how should I fix and configure it properly.
Thanks a lot!