I know the aftermarket ECUs are used for more flexibility and the reflashes are pretty much plug and play but all these options are few if any right now.
Is there any reason why not just go with a fuel controller (Ex: Apexi SAFC) and an ignition controller (Apexi ITC)? I mean, all you want to control basically is the fuel and timing right? It's not as flexible as an aftermarekt ECU but those are high $$$ and difficult to install. The plug-n-play reflashes are few if any (besides Yoshio) and there are still a lot of doubts about the Torque chip and ProECM.
Need more fuel, add some with the SAFC. Need timing pulled due to nitrous or added for use with higher octane, adjust with the ITC. And so forth!