Righto... continuing the build of the ECU and I'm up to the point where the stock ECU case is now gutted and the connector block desoldered from the original circuit board - I hacked, cut and mangled it pretty bad to get it off the connector, but the end result was good - all the connector pins are healthy and intact.
The new MS3 module will fit, but I do need to create some standoff brackets so that it is well secured and pro-like. I could just pack the module with silicone and/or leave it free floating, but I'd like to do this properly and I think a few plastic plates made with the Dremel won't take too long to whip up.