Actually, I think the problems started before the McD merger - it started when Phil Condit became CEO - perhaps the best (that is, WORST) example ever of the "Peter Principle" (simple put, someone will get promoted to their level of incompetence).
The saying in Seattle is that Condit allowed McD to buy Boeing with Boeing's money. It's too close to being true for it to be a joke.
Before Condit - I never heard upper management announce that making money was more important than making a great product - the assumption being that if we made a great product, we'd make money. After Condit became CEO, it was pretty much assumed that we'd never build another new aircraft - Boeing would become 'derivatives are us' because new airplanes cost too much. That worked brilliantly on the 757-300 and 767-400 - NOT (both were massive money losers)

. Since that worked out so well, our new McD based management launched the 787 using the same outsourcing strategy that had worked equally brilliantly on the MD-95/717

. Scuttlebutt is that the MD95/717 program was such a train wreck that if Puget Sound hadn't bailed Long Beach out, the 717 would never have been certified.
There was also considerably dismay that those running the company knew so little about Boeing history that they didn't know that there had already been a Boeing 717 - it was the internal Boeing nomenclature for the KC135.

Pretty much everyone in the company NOT involved in the 787 program recognizes how screwed up it is. Sadly the 787 has managed to insulate themselves from rational thought and continue to believe that the 787 way is the only way to do things.

Worse, the F-ed up processes that they created are being migrated to other healthy programs. I've been personally shocked at how many 'lessons learned' that the 787 has managed to 'unlearn'.
That's the bad news. The good news is that there are signs that current management has recognized the error of their predecessors ways. Outsourcing is being scaled back. BC (Before Condit), Boeing was an engineering company that built airplanes. DC (During Condit - and Stonecipher), Boeing management insisted that it was a manufacturing company that happened to do engineering

. Upper management has recently said - in so many words - that Boeing IS an engineering company that builds airplanes.
So the signs are that those at the top have decided to change course - but Boeing is a massive ship that takes a long time to change direction. The iceberg is looming - only time will tell if we've actually changed course, or if the announcement of "Iceberg RIGHT AHEAD!" was met with "right, now lets 5S those deck chairs