Customs in European airports is generally very quick, just a matter of going through a special door, unless you have something to declare or unless they suspect you of something. Passport control is generally pretty quick as well.
There's also the possibility that you'll have to be re-screened for security. The only info I could find is really old, but suggests that there's no re-screening at Munich: http://www.flyertalk.com/forum/practical-travel-safety-issues/1587052-airports-require-you-reclear-security-international-transit.html
I'd be more worried about possible delays of the first flight than about time to go through the formalities.
Also take a look at http://www.munich-airport.de/en/consumer/aufenthalt_trans/airportstop/minconntime/index.jsp - they talk about 30 / 35 minute connections. (By the way, are you connecting within the same terminal? This is something to consider as well).
Obviously, I wouldn't buy two separate tickets that are so close together, but as long as both flights are on the same reservation, I think you should be ok.