Interesting stuff, that's a lot of work you've put into developing that prototype.
I see that the early Denso ECU is your weapon of choice to mod and remap, is EGR removal something you've dealt with before? I assume you would need to enrich the mixture at overrun to compensate for the lean condition during vacuum.
I would like to design a more efficient intake manifold with tuned inlet tract length to make the most of the available torque (fluid mechanics is my thing), would be a much cleaner set up without the EGR.