New ECU is in, not sure if I was doing something wrong but took 4 attempts to get it to actually sync as detailed above. Not sure if it made any difference, but entered the EKA using Nanocom on the last try.

Suspect the battery is a bit flat which may not have been helping either. But its now running on all cylinders again. Now to just properly fix the wiring which was bypassed to eliminate the gas ecu from being the problem.

I have a NAS P38 2001, and want to replace ECU by an european ECU to get rid of SAI.

Do all NNN100660 contain same firmware?
Does it matter if the new ECU has been in a manual transmission car, whereas I have an automatic version?

Can I change needed settings with Nanocom, if I just get some NNN100660?

The NNN100660 should be a straight swap for your NNN100600 which is the one used with SAI, you'll just need to copy over the code as detailed earlier. I suspect they are all very much the same just with different firmware depending on whether you have SAI or not. No mention of a different one for auto or manual but if they were different, you'd be hard pressed to find one for a manual, a V8, particularly a late model, with a manual gearbox is a bit into hens teeth territory.

I've actually got a NNN100660 that was bought to try to see if it cured a problem on another car that is from a 1999, 4.6, automatic and is a known good one. If you don't find one, drop me a PM as both my cars are GEMS.