I just did this fix a couple weeks ago on my 06 S2R. Started with the moto stalling intermittently. Mechanic said next time it stalls take the key out and key back on but do not start. If no fuel pump whirring sound, it's not priming. Looked up all the old threads here and saw it was usually the red wire under the factory epoxy in the wiring harness. I figure even if I mess up taking out the old unit and trying to fix it, I'll be the one installing in the new $1200 part so might as well try. Sucks I just filled the tank right before it happened. Anyway here's my fix:
1. Took out the factory unit and disassembled as described in the other threads.
2. Close up of the internal side of the wiring harness. You can see how the factory epoxy has disintegrated. Took the multimeter to test the 4 wires through the harness while wiggling the wires. No surprise, the RED wire to the fuel pump is the weak link.
3. The only difference with using the new wiring harness 51020032A, it does not have the extra ground wire for the fuel level sensor/connection to the fuel filter mounting tab. So the shop where I bought the new harness backed out the factory ground at the fuel pump connector, and made a new connection at the fuel pump plug. Here is a pic of the removed factory ground wire:
4. Here you can see the old harness on the left and the new harness on the right with the extra ground wire connected to the new fuel pump plug:
5. Everything back together with a new fuel filter.
6. Here's a close up of the extra ground wire they added to the fuel pump plug. The female connector must not have been a 100% direct match or maybe they had too much wire where they crimped the new connector. It was a super tight fit but it's not backing out at this point.
I know I could have tried the JB Weld fix on the old harness but I didn't really trust my soldering skills and I didn't get a reply when asking about which JB Weld to use (if it even makes a difference
http://www.ducatimonsterforum.org/index.php?PHPSESSID=6s436ka7kqv5ogm7h5s8dvnko6&topic=70789.msg1323074#msg1323074)
So all in all I spent $140 on the new harness, $20 for the shop to add the extra ground, $67 for the new fuel filter and o-ring for the flange. So far it's started up every time with no problems, I've run 2 full tanks through and the fuel light comes on at about 130 miles. I know I could've gone with a cheaper fuel filter but with this being the first time I've ever attempted a fuel related fix, I was trying to keep all the variables to a minimum.
If it wasn't for all the help and information on this site, I'm sure I would've had a $1200 fix on my hands. The only used assemblies I found on eBay at the time were $450-$500. Even going with a used part, how can you tell how much longer that will last? The factory one lasted me 59,000 miles. Even though I have no ethanol free gas near me, and I've gone through the headache of the swelling plastic tanks, I hope this new wiring harness lasts just as long.