score:4
That's a tricky one. As it appears you already know you must apply to the country that's the main destination of your trip. Finding out what that is is the problem here.
Going just by the itinerary you have sketched it would sound like Germany is your main destination -- it's both where you spend most of the time and where the conference is.
However, you also mention that a university in the Netherlands is paying for your travels -- for some reason we don't know, but it must be pretty important, which strongly suggests that the Netherlands is your actual main destination.
If you apply to Germany, they're going to be confused why the Dutch university is paying for your tickets (since you must disclose in the application how the trip is funded).
On the other hand, if you apply to the Netherlands, being funded by the Dutch university is a strong reason why that actually is the main destination of the trip, so they should not have any reason to think you're consulate shopping (which is the main reason for getting into trouble in these cases).
Personally I would pick the Netherlands, but a case could also be made for Germany. Arguably the most important thing right now is that you pick one and get an application in as soon as humanly possible -- you're somewhat late already, but not so late as to be hopeless.
And yes, no matter where you apply, you must provide an itinerary and documentation for your entire visit to the Schengen area, not just for the part of it in the country whose consulate you're applying to.