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I realized there aren't yet any binary distribution of ROS for most of the operating system and, [..] also for Ubuntu 16.04

ROS on Ubuntu is one of the combinations that is very well supported by the binary releases.

I realized there aren't yet any binary distribution of ROS for most of the operating system and, [..] also for Ubuntu 16.04

ROS on Ubuntu is one of the combinations that is very well supported by the binary releases.

I realized there aren't yet any binary distribution of ROS for most of the operating system and, [..] also for Ubuntu 16.04

ROS on Ubuntu is one of the combinations that is actually very well supported by the binary releases.

Unless you have a very strong desire or need to install Indigo on Ubuntu Xenial (16.04), I would recommend you install ROS Kinetic, following the regular installation instructions that will use the provided binary packages. This should be a 5 minute affair in most cases.

So I decided to build ROS Indigo from source by following this guide [..]

If you really must use ROS Indigo, either install Ubuntu Trusty (14.04) and again follow the regular installation instructions, or build it from sources, but be prepared to have to deal with (potentially) lots of dependency problems.

I don't feel it makes sense now to go through the rest of your post and try and diagnose your current issues before you've decided which course of action is appropriate for you and explained why.