You have a couple of options, but first here's what most likely happened.
The 6 pin firewire connector carries both POWER and signal. When it's plugged in upside down power is applied to the signal lines which usually results in blowing the interface chip in the unit where the plug was reversed.
See > FireWire Port Failures in Host Computers and Peripheral Devices
http://www.wiebetech.com/whitepapers/Fi ... ilures.php
"4.2.2.1 PORT FAILURE BY REVERSE INSERTION
In this scenario, the user inserts the cable with the connector twisted 180 degrees. An examination of the FireWire six pin ports suggests that this is not possible, but it has actually been done many times. It is more likely to happen when the port is worn, or when the port easily "spreads" when reverse inserted. Some FireWire ports are built with the metal seam at the narrow end of the port, making it much easier to reverse insert the cable. The resulting (errant) electrical connections cause Power lines to be directly connected to Data lines. This invariably fries the PHY attached to that port."
As far as repair:
You can send the unit to MOTU. I'm not sure what the current cost is for this. All I could find was this:
http://www.gearslutz.com/board/low-end- ... nking.html
"the charge for the repair is 125 Euro" <Posted 14th November 2011
"After talking to Motu tech support (I got a reply after 1 day) I sent the device to the distributor in Germany. They said that the board is fried (Probably because I connected the FW cable once up side down - The port is pretty wide so you can connect it both ways... flaw of design + reckless user). I had to spend a bit for the repair, I think that in the US they do it for 99$." <Posted 28th November 2011
The chip that needs replaced is a $3.00 part! (
http://avnetexpress.avnet.com) BUT, it is a 64 pin device and not easy to replace unless you have the right equipment to work with surface mount parts. I do NOT have the proper equipment and HAVE replaced parts like this but it was NOT EASY and one stands a VERY good chance of damaging the circuit board without the right equipment.
You can also request a FREE SAMPLE up to quantity 3 from
http://www.ti.com/product/tsb41ab2.
Here is a photo of the device which is located right behind the firewire connectors. This is from my own MOTU Travler which has one damaged firewire port as I type this:
Closeup of the device:
Maybe someone that has a recent experience getting this repaired by MOTU can let us both know how much it cost for them to do it.
If you get a price from MOTU on this PLEASE let me know what they are currently charging for this repair as I now have an 828mk2 and an 896Mk3 with only ONE working firewire port and I'm not sure I want to risk damaging the device by trying to repair it myself, especially since one port is still working at this time. If like you, BOTH ports were dead I might give it a try as I do have some experience with replacing surface mount devices...