Upgrade from 3.5.0rc1(build 1) to 3.8.0(build 1)

Hi all,I want to upgrade my site from PHPFox 3.5.0 to 3.8.0 and we have lot of custom modules and also we have changed the code of core files too.Can you tell me, how to upgrade it to latest version? and we don't want to lose any data on our site.