My two penneth on some of the points/questions:
Morgan have used the same S&S ECU for all 10 years of production P/N 55-0732. I believe so.
Earlier ECU's used USB Mini B type, later ones use USB-C. - yes
Morgan lock the ECU when programmed and there is no way to unlock a locked ECU. - yes, you need the unlock code which only Morgan have. (S&S probably have the code as well but won't disclose it).
The software on the ECU is loaded via a 'box file' (mapping). - yes
The Box File for Euro 3 and Euro 4 M3W's are different. - yes, based on the experience of AndyJazz
Euro 4 M3W's modified to Euro 3 look are fitted with Euro 3 mapping. - again, based on the experience of AndyJazz this is likely to be the case
Stage 1 upgrades (exhaust & air filter) will run on a standard locked ECU. - yes
Stage 2 upgrades (exhaust, air filter and 569 cams) require an unlocked ECU and appropriate box file, ideally adjusted on a dyno - yes.
Note, Stage 2 will run on the standard, locked ECU but will throw up engine check light and fault codes as the fuelling goes out of the ECU adaptive range.
S&S Unlocked ECU's are unavailable (possibly long term).This is undetermined. At the moment there seems to be no more unlocked S&S ECU's available but we don't know whether there may be more produced. An existing locked ECU could be unlocked with the appropriate unlock code. It's worth noting the ECUs are locked to comply with national emissions regulations and once the M3W goes out of production (next month?) we may be able to persuade MMC to provide the unlock code.
G56 have the Emerald alternative programmable ECU mapped for stage 2 upgrades. - yes, they can supply an Emerald ECU with a M3W Stage 2 map although this is currently out of stock. The Emerald ECU can be bought direct from Emerald, the key is the map.
Krazy Horse say they 're-flash' the ECU but how do they re-flash a locked ECU?They don't, they flash an unlocked ECU and when on the dyno they live tune it.
Questions -
Is there base software on the ECU that you upload the box file to?The S&S unlocked ECU is supplied with a number of standard base maps based on check box options. For example 596 cams yes/no. The standard KH Based map and Stage 2 maps are out in the TM community and can be emailed around for upload to an unlocked ECU using Protune.
Is that software available on the S&S website? Not that I'm aware of. Protune is available via the S&S site but you'll need a suitable M3W box file
Is the base software different for Euro 3 and Euro 4 cars or is it the same?Different to meet the EU3 vs EU4 emissions regulations. A EU3 car is mapped for 82 bhp, 140 Nm torque, 215 g/Km CO2 whilst a EU4 is mapped for 68 bhp, 129 Nm, 187 g/Km CO2
Are there any other alternatives to an (unavailable) S&S unlocked ECU other than Garage 56? -Yes, there are several aftermarket ECUs but I don't know of any with a S&S map.