Worst Case Scenario
You may have trouble boarding your flight in Munich because technically your visa is not valid for your arrival time, so they may not let you board the plane in Munich. They will check your visa at the gate while you try to board the plane. They may not catch it, but they could. Be prepared to take another flight, if they decide you can't board. It will be at their discretion, and if you're there at weird hours, they may not have many people on staff to make the correct decision in your favor.
Hopefully you speak some German or Russian, as English gets more and more scarce the closer you go towards Russia. They (Lufthansa) had to find a man in the terminal who could speak English, for me, to check my visa. Worst case is you take a later flight.
I highly advise you to contact your carrier to see if they'll allow you to board. It shouldn't be a problem, but it could be. Domodedovo is very slow at clearing customs, because of the volume of passengers on arrival flights.
In Germany, they will bus you to a tiny terminal, far away from normal passengers. I had to sleep a few hours in terminals like this, all over Europe when visiting Russia. Be prepared to wait and to be far away from any cool terminals that have nice stuff like coffee or restaurants. You will be sectioned off for security reasons (I believe). They keep you in the freezing cold (in the winter) and I had a hard time finding a place to even charge my phone (in Frankfurt). They also have to bus you to those terminals and to the plane, because you are so far removed from any real airport amenities.
Domodedovo (DME) arrival
Domodedovo takes forever to clear customs. I took a similar flight, from Frankfurt and arrived very late, just like you will.
My advice is never fly to Domodedovo, as the customs there is a free for all. If you aren't prepared for it, please do get ready for the zoo.
You must realize that there are no real lines. You will be forced into non-Russian citizen lines, only to get pushed out of those lines, whenever Russian citizens are tired of waiting in their lines. Which is often.
It's a very different process than USA customs clearing. In USA, the visitor is given preference and good treatment, whereas in Russia, you are pushed aside and they wave their Russian passports in your face. They will also use their children to cut in line in front of you.
Sheremetyevo (SVO) is the better airport
Sheremetyevo is much easier for clearing customs. If you travel to Domodedovo, it'll take you 2 hours just to get to that counter. Be warned. I have never had it take less than 1 hour at Domodedovo. I've had it take 3 hours before too. It's never consistent and it depends on what hour you arrive and who is working. I have had the same customs officer (a young man) twice in a row now, and he never smiles and never is friendly. Hopefully you get lucky and there are only a few planes unloading during your time, so it's faster. There are many factors in place, but expect 1-2 hours for customs at Domodedovo, always.
Sheremetyevo airport in Moscow has never taken me more than 30 minutes to clear customs. It is much easier, cleaner, modern and the people are much nicer there. My two cents.