So Like many others I was going crazy trying to get the OS to update. I had done everything recommended with settings in the B and in SysEx Librarian and Logic. The unit showed SE in the top left so I knew it was getting data... it just wasn't getting *good* data.
In this case I was using a USB->MIDI adapter from eBay. most of these appear to all be the same, at least as far as the cheap ones vs what appears to be the same unit with a brand name on it. It works fine for regular midi things - I can play something on my sequencer to soft instruments on the laptop just fine.
I spent many hours messing with settings in SysEx with no luck.
Then I got a Tascam 20X20 USB interface with MIDI on it... ok... lets try that ?
Well the Tascam MIDI interface worked perfect with SysEx on 2nd try. I had to get the correct port selected, and set the packet delay interval to 350ms. I left the interface on full speed. It took quite a while for it all to upload, but the B counted segements and packets. When it completed, hit STORE, and it did its thing writing the OS into the Flash ROM. Booted up to 4.9 and all seems happy.
So the problem may not be your software at all... but your MIDI interface. I suspect the USB -> MIDI adapter was doing something bad to the SysEx data somehow which the Tascam didn't. I know buying a brand name new MIDI interface or I/O device isn't what you want to hear, but you can always borrow, go to a friends place, etc and try out different MIDI hardware on the computer side.