I also believe that in warmer conditions, say outside temps of 85 degrees F or higher, and over 75% humidity, the charging option may cause the back to heat up excessively and that REALLY created a lot of noise. Back in September, I was doing a shoot, at iso 50, which most times is very clean even with a 1.5 stop push, and on image review, I noticed that the images were all very noisy. While reviewing, I noted that my 260 was very warm to the touch. At that time I was doing a low/slow (I can't remember which term is used) to the back. I stopped this, and quit my shooting for 10 minutes, allowed the back to cool off, and then image quality returned.
On my 260, USB3 port is a bit tricky, in that if I happen put any movement on where the cable is inserted to the back, I can get a error, and no connection message.
I use a 6 foot and 9 foot cable in the field.
I only briefly tried the FW800 connection on a Macbookpro 15" and did not do a enough shoots to really see if the speed was equal or greater than USB3.
I do find that the USB3 connection to my S Pro 2 is very quick, so much so that I hate going back to the LCD and waiting on the view to refresh to 100% and back.
I can also see your cable length issue being a problem, however I have found that to be a problem with printers also, as most devices seem to spec at the 9 foot length.