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There are a few things for you to consider in this endeavor. The first is that, for the most part, upgrades can only be granted on the airline where you have the miles. There are exceptions to this but they generally require having purchased the most expensive fares which will likely blow your beer budget and that doesn't bode well for an Oktoberfest trip. The second is that the time you are traveling is peak season for MUC so getting an upgrade might be hard to do.

You mention having a lot of miles in the CO program so I'd start with them. Since they do not fly to MUC you'll have to find an itinerary with the transatlantic flight on CO metal and then a connection, likely on KLM via Amsterdam or on Air France via Paris, to get all the way to MUC. You can use the Continental website to search for trips with upgrade availability (just search to AMS or CDG) and then see what it would price out to get the ticket that has those flights in it. That is probably a bit more complicated than it sounds (and it doesn't sound all that easy ) but it can be done. An upgrade on Continental is also going to require a co-payment of cash in addition to the miles, so that is probably going to skew your budget a bit.

You might be better off just looking for a straight award ticket for the trip. You've got enough miles in the AmEx + CO combined to do coach one way and business the other, assuming availability. And with a bit of work on the AmEx front you might be able to get enough for a reward in Star Alliance that could potentially get you on the Lufthansa non-stop flight.

If you have specific dates in mind (and it sounds like you do) sharing them might help some folks here work with you to craft some specific plans.