Greg Nelson, who has had the thankless job of running MSN for Microsoft, has left that position and been given the even more thankless task of running the integration of the complex search and online advertising partnership struck by the software giant and Yahoo.

Nelson’s counterpart at Yahoo, according to sources, will be Mark Morrissey, who is currently SVP of Products at the Internet giant.

The pair–pictured above, with Morrissey on left, Nelson on right–will have their hands full in what will ultimately be a two-year effort.

BoomTown’s title for the relationship: A Couple of White Geek Guys Sitting Around Arguing!

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Just after he got the job 10 days ago, BoomTown got the chance to chitty-chat a bit with Scott Moore, the former Yahoo media chief, who is returning to Microsoft, where he will lead its online content efforts for the U.S for its MSN online service.

Apparently, you can go home again!

It’s a touché tale because it feels like Moore was pretty much rehired by MSN exec Greg Nelson (also in on the conversation with Moore) to give Yahoo a wallop where it really will hurt–its powerful content business, one of Yahoo’s only bright spots.

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In an unusual homecoming and odd job switcheroo between two Internet execs, former Yahoo media head Scott Moore is returning to Microsoft to lead its content efforts, according to many sources both inside and outside the company.

Moore will become U.S. executive producer, responsible for leading the content and programming strategy for the MSN online service. He will return to Microsoft’s Seattle area HQ in mid-March and report to Greg Nelson, GM of the MSN Global Media Group.

Moore left Yahoo late last year due to unhappiness over the turmoil at the company and to pursue a start-up idea he had.

He was replaced at Yahoo–in a rushed appointment–by Jeff Dossett, who came, wait for it, from Microsoft, where he held the job Moore is now taking.

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According to several sources, more restructuring is about to hit Microsoft’s online division as various departments are moved among and between its top execs, with changes to be announced as early as today.

While BoomTown is still gathering information, it looks like longtime Microsoft exec Yusuf Mehdi, who is now in charge of marketing, online audience business development and product management for MSN and the search properties, will get more added to his portfolio, including overall business development for the online properties.

Mehdi could eventually get purview over programming for MSN too, said several sources.

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Why settle for less, when you can have the whole enchilada? Thus, here is the entire MSN rejiggering memo I wrote about earlier today.

It was penned by Greg Nelson, head of the MSN Global Media Group, who reveals in it–interestingly–that he has not yet filled the job of U.S. Executive Producer of Microsoft’s consumer online service.

Also, a note to “note taker” at the Town Hall meeting next Tuesday at Microsoft HQ to discuss the changes, who is mentioned below: You can email me those meeting notes you are apparently taking here and I promise not to tell anyone (well, to tell you the truth, I will tell everyone).

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Here’s part of an internal memo BoomTown obtained about some small, but interesting, changes at Microsoft’s MSN unit, sent out by the GM of its Global Media Group, Greg Nelson, which is under the leadership of–well, frankly–a confusing panoply of people.

That’s why I have been haranguing Microsoft CEO Steve Ballmer for a little digital clarity, especially around its consumer digital businesses and brands.

Ballmer has been searching for an overall head of that business, and it will fall to the person he ultimately selects as digital head to figure out what to do next.

Until then, let’s rearrange some chairs!

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