Are you running a WBO2? The Innovate setup is pretty cheap and seems to work well. I have a DataEdge ready for an old carb bike ('84 Honda VF1100s) but I haven't installed it yet. I'll let you know if it works well.
No need for the MS, if you're tuning the stock box I'd figure the Ostrich is a better solution. Unless the definition is wrong, eh? I'd think an MS-based standalone would be easier with the software but more trouble with the OEM hardware.
Did you compare your bin to any others? I know it's unlikely that anyone would have your setup, but you might get headed in the right direction that way. There are a lot of interdependent maps in the Motronic, getting one wrong would snowball.