Not only did Mahler change the order of the middle movements several times, there are conflicting reports about what his last thoughts were. I'm not sure I have a preference... It can work either way, although it changes the overall feel of the piece. If the conductor goes for the scherzo 2nd, I certainly like a contrast. Sinopoli contrasted them nicely, going for a slow, somewhat ponderous 1st mvt and a really snappy scherzo.
As for the 'hammer blows' in the finale, Tilson Thomas has a nice solution: a large wooden box with a hole in the front, banged on top with full force by a sledge hammer. It makes quite an impact when heard live, and also on his recording. Benjamin Zander uses something similar (though I haven't actually seen it). I believe it involves a large box or block being struck with a heavy lead pipe. It has fantastic impact on his recording.
I still stand by the idea that Jar & I had years ago: Best thud for the hammer blow would be for an enthusiastic Mahler fan to run up to the balcony of the concert hall and jump off to make the thud. It would be a bit rough on the fan, though, especially if all three hammer blows are done (not to mention the patrons sitting where he or she lands).