I don't know what the part number difference is if their is any. I noticed this before. If you put the one part number in it superceeds to the other new part number. You can switch both ecu part numbers back and fourth between other 05-06 gsxr 1000's and they run fine.
I was selling a ecu on ebay and some guy asked because it had a different part number then his. If you are looking for a ecu shoot me a pm. I have one for sale.
Google translates that as "Do you use a harness?" If you mean what harness is used, the immobilizer models (E2, E19, and E24) use the 36610-41G10 harness while the others use 36610-41G30. The immobilizer ignition switch is also different. The key for an immobilizer model has a RFID that must match the individual ECM, not just the part number.
As best I understand this, you had a 32920-41G50 that failed so you replaced it with a 32920-41G20 and now it won't start. The problem is probably not with the wiring harness. Instead it's more likely that the 32920-41G20 did not come with a matched key and you're trying to use the key for the 32920-41G50. That won't work unless you're really lucky (you aren't). Instead you must either reprogram the key to match the new ECM, buy a new key that matches the new ECM, or flash the ECM to turn off the immobilizer checking. Here's someone who does that. It's not cheap so I'd try to first make sure that it's your problem. Perhaps there's someone closer to you who does it. Note that the key cuts must match the tumblers on the ignition switch and the key's RFID must match the ECM.
A first step would be to compare the flashing codes on the cluster's immobilizer indicator with those on 9-22 of the service manual. It sounds like you're getting the fast flashing that indicates that the key ID is not being recognized.
In general, you should never buy an immobilizer ECM unless it comes with a matched key. Furthermore you should get a duplicate matched key made and store it in a safe or somewhere secure so that you don't have to go through all this if the original is lost or damaged.
P.S. If indeed the problem is that you don't have a matched key for the new ECM, it may be cheaper to start over and buy another ECM that comes with the key. Then go to a locksmith or someone who duplicates immobilizer keys and have them copy the RFID from your new key to your current key. What I'm saying here is that it's my impression that making a key from scratch for an ECM that doesn't have a key will cost about as much as buying an ECM with a key. It's sufficiently difficult and expensive that Suzuki recommends buying a new ECM if all keys are lost on an immobilizer model.